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(-) Description

Title :  CRYSTAL STRUCTURE AND RAMAN STUDIES OF DSFP483, A CYAN FLUORESCENT PROTEIN FROM DISCOSOMA STRIATA
 
Authors :  G. D. Malo
Date :  05 Mar 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F  (2x)
Keywords :  Beta Barrel, Chromophore, Luminescence, Photoprotein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. D. Malo, M. Wang, D. Wu, A. L. Stelling, P. J. Tonge, R. M. Wachter
Crystal Structure And Raman Studies Of Dsfp483, A Cyan Fluorescent Protein From Discosoma Striata.
J. Mol. Biol. V. 378 869 2008
PubMed-ID: 18395223  |  Reference-DOI: 10.1016/J.JMB.2008.02.069

(-) Compounds

Molecule 1 - GFP-LIKE FLUORESCENT CHROMOPROTEIN DSFP483
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109(DE3)
    Expression System Vector Type: PLAMSID
    Organism Common: STRIPED MUSHROOM
    Organism Scientific: DISCOSOMA STRIATA

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABCD  
Biological Unit 2 (2x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1CRQ5Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
2NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CRQ4Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CRQ2Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
2NA-1Ligand/IonSODIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:176 , ASP C:176BINDING SITE FOR RESIDUE NA A 233
2AC2SOFTWAREASP B:176 , ASP D:176BINDING SITE FOR RESIDUE NA B 233

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:106 -B:106
2C:106 -D:106

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:52 -Pro A:53
2Phe A:87 -Pro A:88
3Gly B:52 -Pro B:53
4Phe B:87 -Pro B:88
5Gly C:52 -Pro C:53
6Phe C:87 -Pro C:88
7Gly D:52 -Pro D:53
8Phe D:87 -Pro D:88
9Gly E:51 -Gly E:52
10Phe E:87 -Pro E:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CGL)

(-) 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:224
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           GFPL_DISST     1 MSCSKSVIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
               SCOP domains d3cgla_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 3cglA00 A:1-226 Green Fluorescent Protein                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgl A   1 MSCSKSVIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFq--NKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
                                    10        20        30        40        50        60     |  70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                                                            66-CRQ                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
           GFPL_DISST     7 VIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
               SCOP domains d3cglb_ 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....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgl B   7 VIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFq--NKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
                                                                                      66-CRQ                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:221
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:223
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
           GFPL_DISST     6 SVIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFYEP 228
               SCOP domains d3cglc_ C: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgl C   6 SVIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFq--NKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFYEP 228
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225   
                                                                                       66-CRQ                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:220
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:222
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226  
           GFPL_DISST     7 VIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFYEP 228
               SCOP domains d3cgld_ D: automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--..............hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3cgl D   7 VIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFq--NKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFYEP 228
                                    16        26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226  
                                                                                      66-CRQ                                                                                                                                                              


Chain E from PDB  Type:PROTEIN  Length:216
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:220
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
           GFPL_DISST     7 VIKEEMLIDLHLEGTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
               SCOP domains d3cgle_ E: autom  ated matches                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee.--..eeeeeeeeee....eeeeeeee........hhhhhh....--hhhhh.........hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgl E   7 VIKEEMLIDLHLEGTF--HYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFq--NKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIKTVYRAKKAALKMPGYHYVDTKLVIWNNDKEFMKVEEHEIAVARHHPFY 226
                                    16     |  26        36        46        56        66  |     76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226
                                          22 25                                       66-CRQ                                                                                                                                                            


Chain F from PDB  Type:PROTEIN  Length:60
 aligned with GFPL_DISST | Q9U6Y7 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:159
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169         
           GFPL_DISST    20 GTFNGHYFEIKGKGKGQPNEGTNTVTLEVTKGGPLPFGWHILCPQFQYGNKAFVHHPDNIHDYLKLSFPEGYTWERSMHFEDGGLCCITNDISLTGNCFYYDIKFTGLNFPPNGPVVQKKTTGWEPSTERLYPRDGVLIGDIHHALTVEGGGHYACDIK 178
               SCOP domains d3cg lf_                      F:  automated                              m  atches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.-...---------------------...-...........-----------------------------.--.eee..-.eee..---------------.eee.....hhhhhh.--------------------..ee.---------.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cgl F  20 GTFN-HYF---------------------TKG-PLPFGWHILCP-----------------------------W--SMHFED-GLCCIT---------------FTGLNFPPNGPVVQKK--------------------DIHHA---------ACDIK 178
                               | | | -         -        49 | |    59   |     -         -         -   |  | 99 | |    |-         -    |  129       139         -         -|   |    -    |    
                              23 | |                    49 | |        63                            93 96  101 |  108             124            139                  160 164       174    
                                25 |                      51 |                                               103                                                                           
                                  27                        53
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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, 6)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GFPL_DISST | Q9U6Y7)
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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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