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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DARK STATE OF KINDLING FLUORESCENT PROTEIN KFP FROM ANEMONIA SULCATA
 
Authors :  M. L. Quillin, D. M. Anstrom, X. Shu, S. O'Leary, K. Kallio, D. M. Chudako S. J. Remington
Date :  04 Oct 04  (Deposition) - 19 Apr 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  B  (2x)
Keywords :  Fluorescent Protein, Chromophore Structure, Ascp595, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Quillin, D. M. Anstrom, X. Shu, S. O'Leary, K. Kallio, D. M. Chudakov, S. J. Remington
Kindling Fluorescent Protein From Anemonia Sulcata: Dark-State Structure At 1. 38 Resolution
Biochemistry V. 44 5774 2005
PubMed-ID: 15823036  |  Reference-DOI: 10.1021/BI047644U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GFP-LIKE CHROMOPROTEIN FP595
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: JM-109
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: SNAKE-LOCKS SEA ANEMONE
    Organism Scientific: ANEMONIA SULCATA
    Organism Taxid: 6108
    Synonym: ASCP595

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1BME7Ligand/IonBETA-MERCAPTOETHANOL
2CRK2Mod. Amino Acid4-{(Z)-[2-[3-(METHYLSULFANYL)PROPANOYL]-5-OXO-1-(2-OXOETHYL)-1,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE]METHYL}BENZENOLATE
3NH22Ligand/IonAMINO GROUP
Biological Unit 1 (3, 22)
No.NameCountTypeFull Name
1BME14Ligand/IonBETA-MERCAPTOETHANOL
2CRK4Mod. Amino Acid4-{(Z)-[2-[3-(METHYLSULFANYL)PROPANOYL]-5-OXO-1-(2-OXOETHYL)-1,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE]METHYL}BENZENOLATE
3NH24Ligand/IonAMINO GROUP
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1BME8Ligand/IonBETA-MERCAPTOETHANOL
2CRK2Mod. Amino Acid4-{(Z)-[2-[3-(METHYLSULFANYL)PROPANOYL]-5-OXO-1-(2-OXOETHYL)-1,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE]METHYL}BENZENOLATE
3NH22Ligand/IonAMINO GROUP
Biological Unit 3 (3, 10)
No.NameCountTypeFull Name
1BME6Ligand/IonBETA-MERCAPTOETHANOL
2CRK2Mod. Amino Acid4-{(Z)-[2-[3-(METHYLSULFANYL)PROPANOYL]-5-OXO-1-(2-OXOETHYL)-1,5-DIHYDRO-4H-IMIDAZOL-4-YLIDENE]METHYL}BENZENOLATE
3NH22Ligand/IonAMINO GROUP

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:61 , CYS A:62 , CRK A:65BINDING SITE FOR RESIDUE NH2 A 240
2AC2SOFTWAREGLY A:143 , THR A:144 , PHE A:194 , ASP A:196 , ARG A:220 , CYS A:222BINDING SITE FOR RESIDUE BME A 250
3AC3SOFTWAREPRO A:10 , PHE A:11 , CYS A:114BINDING SITE FOR RESIDUE BME A 251
4AC4SOFTWAREPRO A:131 , CYS A:164 , ARG A:168 , HOH A:407 , HOH A:469BINDING SITE FOR RESIDUE BME A 252
5AC5SOFTWARELYS A:42 , ILE A:43 , GLU A:44 , CYS A:210BINDING SITE FOR RESIDUE BME A 253
6AC6SOFTWARESER B:61 , CYS B:62 , CRK B:65BINDING SITE FOR RESIDUE NH2 B 240
7AC7SOFTWAREGLY B:143 , THR B:144 , PHE B:194 , ASP B:196 , ARG B:220 , CYS B:222BINDING SITE FOR RESIDUE BME B 250
8AC8SOFTWAREPRO B:10 , PHE B:11 , CYS B:114BINDING SITE FOR RESIDUE BME B 251
9AC9SOFTWARELEU B:162 , CYS B:164 , ARG B:168 , LEU B:170 , HOH B:399 , HOH B:414BINDING SITE FOR RESIDUE BME B 252

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XMZ)

(-) 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 1XMZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XMZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1XMZ)

(-) 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
 aligned with NFCP_ANESU | Q9GZ28 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:229
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223         
           NFCP_ANESU     4 FLKKTMPFKTTIEGTVNGHYFKCTGKGEGNPFEGTQEMKIEVIEGGPLPFAFHILSTSCMYGSKTFIKYVSGIPDYFKQSFPEGFTWERTTTYEDGGFLTAHQDTSLDGDCLVYKVKILGNNFPADGPVMQNKAGRWEPATEIVYEVDGVLRGQSLMALKCPGGRHLTCHLHTTYRSKKPASALKMPGFHFEDHRIEIMEEVEKGKCYKQYEAAVGRYCDAAPSKLGHN 232
               SCOP domains d1xmza_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 1xmzA00 A:4-232 Green Fluorescent Protein                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--......ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..............ee..eeeeeeee..eeeeeeeeeee.....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee--..eeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xmz A   4 FLKKTMPFKTTIEGTVNGHYFKCTGKGEGNPFEGTQEMKIEVIEGGPLPFAFHILSTSC--mSKTFIKYVSGIPDYFKQSFPEGFTWERTTTYEDGGFLTAHQDTSLDGDCLVYKVKILGNNFPADGPVMQNKAGRWEPGTEIVYEVDGVLRGQSLMALKCPGGRHLTCHLHTTYRSKKPASALKMPGFHFEDHRIEIMEEV--GKCYKQYEAAVGRYCDAAPSKLGHN 232
                                    13        23        33        43        53        |- |      73        83        93       103       113       123       133       143       153       163       173       183       193       203 |  |  213       223         
                                                                                     62  |                                                                                                                                         205  |                        
                                                                                        65-CRK                                                                                                                                        208                        


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with NFCP_ANESU | Q9GZ28 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:236
                                1                                                                                                                                                                                                                                       
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226      
           NFCP_ANESU     - ----MASFLKKTMPFKTTIEGTVNGHYFKCTGKGEGNPFEGTQEMKIEVIEGGPLPFAFHILSTSCMYGSKTFIKYVSGIPDYFKQSFPEGFTWERTTTYEDGGFLTAHQDTSLDGDCLVYKVKILGNNFPADGPVMQNKAGRWEPATEIVYEVDGVLRGQSLMALKCPGGRHLTCHLHTTYRSKKPASALKMPGFHFEDHRIEIMEEVEKGKCYKQYEAAVGRYCDAAPSKLGHN 232
               SCOP domains d1xmzb_ B: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains 1xmzB00 B:-3-232 Green Fluorescent Protein                                                                                                                                                                                                   CATH domains
           Pfam domains (1) -----GFP-1xmzB01 B:2-222                                                                                                                                                                                                          ---------- Pfam domains (1)
           Pfam domains (2) -----GFP-1xmzB02 B:2-222                                                                                                                                                                                                          ---------- Pfam domains (2)
         Sec.struct. author ....hhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--......ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..............ee..eeeeeeee..eeeeeeeeeee.....eeeeeeeeeeee..hhhhh.....eeeeeeeeeee..--..eeeeeeeeeee............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xmz B  -3 HHHGSASFLKKTMPFKTTIEGTVNGHYFKCTGKGEGNPFEGTQEMKIEVIEGGPLPFAFHILSTSC--mSKTFIKYVSGIPDYFKQSFPEGFTWERTTTYEDGGFLTAHQDTSLDGDCLVYKVKILGNNFPADGPVMQNKAGRWEPGTEIVYEVDGVLRGQSLMALKCPGGRHLTCHLHTTYRSKKPASALKMPGFHFEDHRIEIMEEV--GKCYKQYEAAVGRYCDAAPSKLGHN 232
                                     6        16        26        36        46        56     |  66        76        86        96       106       116       126       136       146       156       166       176       186       196        |- |     216       226      
                                                                                            62  |                                                                                                                                         205  |                        
                                                                                               65-CRK                                                                                                                                        208
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 2)

Asymmetric Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NFCP_ANESU | Q9GZ28)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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 Related Entries

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        NFCP_ANESU | Q9GZ28: 1xqm 2a50 2a52 2a53 2a54 2a56 3cfa 3cff 3cfh

(-) Related Entries Specified in the PDB File

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