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(-) Description

Title :  CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, GREEN FORM
 
Authors :  I. Hayashi, H. Mizuno, A. Miyawaki, M. Ikura
Date :  03 May 06  (Deposition) - 08 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (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, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CR82Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2NI4Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CR84Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:7 , LYS B:30 , HIS B:32 , HOH B:486 , HOH B:529 , HOH B:611BINDING SITE FOR RESIDUE NI A 403
2AC2SOFTWAREHIS A:201 , HOH A:593BINDING SITE FOR RESIDUE NI A 404
3AC3SOFTWARELYS A:30 , HIS A:32 , HOH A:490 , HOH A:511 , HOH A:566 , HOH B:589BINDING SITE FOR RESIDUE NI B 405
4AC4SOFTWAREHIS B:201 , HOH B:590 , HOH B:591 , HOH B:599BINDING SITE FOR RESIDUE NI B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GW3)

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GW3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GW3)

(-) Exons   (0, 0)

(no "Exon" information available for 2GW3)

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

    Alignment length:221
                             1                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
         Q8I6J8_TRAGO     - -MSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAFHYGNRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
               SCOP domains d2gw3a_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gw3 A   0 PMSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAF-h-NRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
                                     9        19        29        39        49        59 | | |  69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
                                                                                        61 | |                                                                                                                                                           
                                                                                          63-CR8                                                                                                                                                         
                                                                                            65                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with Q8I6J8_TRAGO | Q8I6J8 from UniProtKB/TrEMBL  Length:225

    Alignment length:221
                             1                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
         Q8I6J8_TRAGO     - -MSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAFHYGNRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
               SCOP domains d2gw3b_ B: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh-.-......................eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gw3 B   0 PMSLIKPEMKIKLLMEGNVNGHQFVIEGDGKGHPFEGKQSMDLVVKEGAPLPFAYDILTTAF-h-NRVFAKYPDHIPDYFKQSFPKGFSWERSLMFEDGGVCIATNDITLKGDTFFNKVRFDGVNFPPNGPVMQKKTLKWEASTEKMYLRDGVLTGDITMALLLKGDVHYRCDFRTTYKSRQEGVKLPGYHFVDHCISILRHDKDYNEVKLYEHAVAHSGL 220
                                     9        19        29        39        49        59 | | |  69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
                                                                                        61 | |                                                                                                                                                           
                                                                                          63-CR8                                                                                                                                                         
                                                                                            65
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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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GW3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GW3)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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        Q8I6J8_TRAGO | Q8I6J8: 2gw4

(-) Related Entries Specified in the PDB File

2gw4 CRYSTAL STRUCTURE OF STONY CORAL FLUORESCENT PROTEIN KAEDE, RED FORM