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(-) Description

Title :  MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 2.0
 
Authors :  S. Pletnev, N. Pletneva, V. Pletnev
Date :  11 Jan 08  (Deposition) - 22 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Far-Red Fluorescent Protein, E. Quadricolor, Chromophore Structure, Ph-Induced Cis-Trans Izomerization, Fluorescent Protein (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

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CIT6Ligand/IonCITRIC ACID
2GOL2Ligand/IonGLYCEROL
3NRQ2Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
Biological Unit 3 (3, 5)
No.NameCountTypeFull Name
1CIT3Ligand/IonCITRIC ACID
2GOL1Ligand/IonGLYCEROL
3NRQ1Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:20 , ASN A:21 , ASN A:125 , PHE A:126 , SER A:128 , HOH A:279 , HOH A:317 , HOH A:318 , HOH A:320 , ALA B:150 , ASP B:151 , GLU B:155 , THR B:177 , ARG B:179 , HOH B:240 , HOH B:310BINDING SITE FOR RESIDUE CIT A 234
2AC2SOFTWAREASN B:8 , GLU B:31 , GLY B:32 , LYS B:33 , THR B:38 , THR B:40 , HIS B:214BINDING SITE FOR RESIDUE CIT B 234
3AC3SOFTWAREASP A:151 , GLU A:155 , THR A:177 , ARG A:179 , ASN B:20 , ASN B:21 , ASN B:125 , PHE B:126 , HOH B:264 , HOH B:277 , HOH B:323 , HOH B:332BINDING SITE FOR RESIDUE CIT B 235
4AC4SOFTWAREASN A:71 , THR A:73 , ASP A:196 , HOH A:283 , HOH A:356 , HOH A:363 , ASP B:223 , LEU B:224 , HOH B:266BINDING SITE FOR RESIDUE CIT A 235
5AC5SOFTWAREGLU A:31 , LYS A:33 , THR A:38 , GLN A:39 , THR A:40 , HIS A:214 , HOH A:350 , SER B:226 , HOH B:361BINDING SITE FOR RESIDUE CIT A 236
6AC6SOFTWARETYR A:14 , LYS A:25 , THR A:27 , PRO B:85 , LEU B:110 , ASP B:112 , GLY B:113 , HOH B:272 , HOH B:326BINDING SITE FOR RESIDUE CIT B 236
7AC7SOFTWAREASP B:98 , ASN B:129 , GLY B:130 , PRO B:131 , HOH B:295 , HOH B:344 , HOH B:365BINDING SITE FOR RESIDUE GOL B 237
8AC8SOFTWAREASP A:98 , GLY A:130 , PRO A:131 , HOH A:292 , HOH A:299 , HOH A:346BINDING SITE FOR RESIDUE GOL A 237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BX9)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BX9)

(-) Exons   (0, 0)

(no "Exon" information available for 3BX9)

(-) 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:225
                                                                                                                                                                                                                                                                 
               SCOP domains d3bx9a_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 3bx9A00 A:2-228 Green Fluorescent Protein                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh......ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx9 A   2 SELITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    11        21        31        41        51        61 ||     73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                        63-NRQ                                                                                                                                                               
                                                                                         66                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains d3bx9b_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains 3bx9B00 B:2-228 Green Fluorescent Protein                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh......ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx9 B   2 SELITENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKVVEGGPLPFAFDILATSFmSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTATQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTEMLYPADGGLEGRSDMALKLVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYCDLPSKL 228
                                    11        21        31        41        51        61 ||     73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
                                                                                        63-NRQ                                                                                                                                                               
                                                                                         66
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BX9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BX9)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1uis RED FLUORESCENT PROTEIN EQFP611
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