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(-) Description

Title :  MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 9.0
 
Authors :  S. Pletnev, N. Pletneva, V. Pletnev
Date :  12 Jan 08  (Deposition) - 22 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (1x)
Biol. Unit 8:  H  (1x)
Keywords :  Far-Red Fluorescent Protein, E. Quadricolor, Chromophore Structure, Ph-Induced Cis-Trans Izomerization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pletnev, D. Shcherbo, D. M. Chudakov, N. Pletneva, E. M. Merzlyak, A. Wlodawer, Z. Dauter, V. Pletnev
A Crystallographic Study Of Bright Far-Red Fluorescent Protein Mkate Reveals Ph-Induced Cis-Trans Isomerization Of The Chromophore.
J. Biol. Chem. V. 283 28980 2008
PubMed-ID: 18682399  |  Reference-DOI: 10.1074/JBC.M800599200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAR-RED FLUORESCENT PROTEIN MKATE
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: XL1 BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTACMAEA QUADRICOLOR
    Organism Taxid: 6118

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A       
Biological Unit 2 (1x):  B      
Biological Unit 3 (1x):   C     
Biological Unit 4 (1x):    D    
Biological Unit 5 (1x):     E   
Biological Unit 6 (1x):      F  
Biological Unit 7 (1x):       G 
Biological Unit 8 (1x):        H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1NRQ8Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 6 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 7 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 8 (1, 1)
No.NameCountTypeFull Name
1NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3BXC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BXC)

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Gly A:49 -Pro A:50
2Phe A:84 -Pro A:85
3Gly B:49 -Pro B:50
4Phe B:84 -Pro B:85
5Gly C:49 -Pro C:50
6Phe C:84 -Pro C:85
7Gly D:49 -Pro D:50
8Phe D:84 -Pro D:85
9Gly E:49 -Pro E:50
10Phe E:84 -Pro E:85
11Gly F:49 -Pro F:50
12Phe F:84 -Pro F:85
13Gly G:49 -Pro G:50
14Phe G:84 -Pro G:85
15Gly H:49 -Pro H:50
16Phe H:84 -Pro H:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BXC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BXC)

(-) Exons   (0, 0)

(no "Exon" information available for 3BXC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxca_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc A   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxcb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc B   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxcc_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.......................eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc C   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains d3bxcd_ D: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bxc D   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226  
                                                                                     63-NRQ                                                                                                                                                               
                                                                                      66                                                                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxce_ E: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc E   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxcf_ F: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc F   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain G from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxcg_ G: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.......................eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc G   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66                                                                                                                                                               


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3bxch_ H: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee...eeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.............hhhhhh....eeeeeeeee....eeeeeeeeee...eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bxc H   5 ITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLP 225
                                    14        24        34        44        54        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216         
                                                                                     63-NRQ                                                                                                                                                            
                                                                                      66
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 8)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BXC)

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  Cis Peptide Bonds
    Gly A:49 - Pro A:50   [ RasMol ]  
    Gly B:49 - Pro B:50   [ RasMol ]  
    Gly C:49 - Pro C:50   [ RasMol ]  
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 Related Entries

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(-) Related Entries Specified in the PDB File

1uis RED FLUORESCENT PROTEIN EQFP611
3bx9 MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 2.0
3bxa MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 4.2
3bxb MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 7.0
3bxc MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 9.0