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(-) Description

Title :  CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, RED FORM
 
Authors :  I. Hayashi, H. Mizuno, A. Miyawako, M. Ikura
Date :  03 May 06  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Beta Barrel, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Hayashi, H. Mizuno, K. I. Tong, T. Furuta, F. Tanaka, M. Yoshimura, A. Miyawaki, M. Ikura
Crystallographic Evidence For Water-Assisted Photo-Induced Peptide Cleavage In The Stony Coral Fluorescent Protein Kaede.
J. Mol. Biol. V. 372 918 2007
PubMed-ID: 17692334  |  Reference-DOI: 10.1016/J.JMB.2007.06.037

(-) Compounds

Molecule 1 - KAEDE
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSETB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: TRACHYPHYLLIA GEOFFROYI
    Organism Taxid: 196280
 
Molecule 2 - KAEDE
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSETB
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: TRACHYPHYLLIA GEOFFROYI
    Organism Taxid: 196280

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1NFA2Mod. Amino AcidPHENYLALANINE AMIDE
2NI4Ligand/IonNICKEL (II) ION
3RC72Mod. Amino Acid{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NFA4Mod. Amino AcidPHENYLALANINE AMIDE
2NI-1Ligand/IonNICKEL (II) ION
3RC74Mod. Amino Acid{(2R)-4-(4-HYDROXYBENZYL)-2-[2-(1H-IMIDAZOL-4-YL)ETHYL]-5-OXO-2,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETALDEHYDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:484 , HOH A:485 , LYS C:30 , HIS C:32 , HOH C:459 , HOH C:470BINDING SITE FOR RESIDUE NI A 438
2AC2SOFTWAREHIS B:201 , HOH B:580 , HOH B:581 , HOH B:602BINDING SITE FOR RESIDUE NI B 439
3AC3SOFTWARELYS A:30 , HIS A:32 , HOH A:458 , HOH A:463 , HOH A:479 , HOH C:486BINDING SITE FOR RESIDUE NI C 440
4AC4SOFTWAREHIS D:201 , HOH D:587 , HOH D:596 , HOH D:597BINDING SITE FOR RESIDUE NI D 441

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GW4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:48 -Pro A:49
2Phe B:83 -Pro B:84
3Ala C:48 -Pro C:49
4Phe D:83 -Pro D:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GW4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GW4)

(-) Exons   (0, 0)

(no "Exon" information available for 2GW4)

(-) 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:62
 aligned with Q8I6J8_TRAGO | Q8I6J8 from UniProtKB/TrEMBL  Length:225

    Alignment length:62
                             1                                                                
                             |       9        19        29        39        49        59  
         Q8I6J8_TRAGO     - -MSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAF  61
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2gw4 A   0 PMSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAf  61
                                     9        19        29        39        49        59 |
                                                                                        61-NFA


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with Q8I6J8_TRAGO | Q8I6J8 from UniProtKB/TrEMBL  Length:225

    Alignment length:159
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
         Q8I6J8_TRAGO    62 HYGNRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gw4 B  63 h--NRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
                            |  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
                            | 65                                                                                                                                                           
                           63-RC7                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:62
 aligned with Q8I6J8_TRAGO | Q8I6J8 from UniProtKB/TrEMBL  Length:225

    Alignment length:62
                             1                                                                
                             |       9        19        29        39        49        59  
         Q8I6J8_TRAGO     - -MSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAF  61
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2gw4 C   0 PMSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAf  61
                                     9        19        29        39        49        59 |
                                                                                        61-NFA


Chain D from PDB  Type:PROTEIN  Length:157
 aligned with Q8I6J8_TRAGO | Q8I6J8 from UniProtKB/TrEMBL  Length:225

    Alignment length:159
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
         Q8I6J8_TRAGO    62 HYGNRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gw4 D  63 h--NRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
                            |  |    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
                            | 65                                                                                                                                                           
                           63-RC7
   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  (0, 0)

(no "SCOP Domain" information available for 2GW4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GW4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GW4)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8I6J8_TRAGO | Q8I6J8)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0006091    generation of precursor metabolites and energy    The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.

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(-) Related Entries Specified in the PDB File

2gw3 CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, GREEN FORM