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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED) VARIANT K70M
 
Authors :  J. L. Tubbs, J. A. Tainer, E. D. Getzoff
Date :  21 Apr 05  (Deposition) - 02 Aug 05  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rfp, Red, Fluorescent Protein, Dsred, Drfp583, Chromophore, Gfp, Coral, Beta Barrel, Beta Can, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Tubbs, J. A. Tainer, E. D. Getzoff
Crystallographic Structures Of Discosoma Red Fluorescent Protein With Immature And Mature Chromophores: Linking Peptide Bond Trans-Cis Isomerization And Acylimine Formation In Chromophore Maturation.
Biochemistry V. 44 9833 2005
PubMed-ID: 16026155  |  Reference-DOI: 10.1021/BI0472907
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN DRFP583
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 562
    Expression System Vector: PET15
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: DISCOSOMA SP.
    Organism Taxid: 86600
    Synonym: DSRED

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (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

(-) Sites  (0, 0)

(no "Site" information available for 1ZGP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological 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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZGP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ZGP)

(-) Sequences/Alignments

Asymmetric/Biological 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:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgpa_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgpA00 A:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgp A   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SMVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    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 B from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgpb_ B: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgpB00 B:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee...eeeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgp B   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SMVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    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 C from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgpc_ C: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgpC00 C:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgp C   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SMVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    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:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
            RFP_DISSP     6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
               SCOP domains d1zgpd_ D: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains 1zgpD00 D:6-225 Green Fluorescent Protein                                                                                                                                                                                    CATH domains
           Pfam domains (1) GFP-1zgpD01 D:6-222                                                                                                                                                                                                      --- Pfam domains (1)
           Pfam domains (2) GFP-1zgpD02 D:6-222                                                                                                                                                                                                      --- Pfam domains (2)
           Pfam domains (3) GFP-1zgpD03 D:6-222                                                                                                                                                                                                      --- Pfam domains (3)
           Pfam domains (4) GFP-1zgpD04 D:6-222                                                                                                                                                                                                      --- Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgp D   6 NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFq--SMVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL 225
                                    15        25        35        45        55        65|  |    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
                                                                                       66-CRQ
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GFP (101)
(-)
Family: GFP (101)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RFP_DISSP | Q9U6Y8)
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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  Cis Peptide Bonds
    Gly A:52 - Pro A:53   [ RasMol ]  
    Gly B:52 - Pro B:53   [ RasMol ]  
    Gly C:52 - Pro C:53   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RFP_DISSP | Q9U6Y8: 1g7k 1ggx 1zgo 1zgq 2h5o 2h5r 2h8q 2v4e 2vad 2vae 4i2y 4kf4 4kf5

(-) Related Entries Specified in the PDB File

1zgo HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED)
1zgq CRYSTAL STRUCTURE OF THE DISCOSOMA RED FLUORESCENT PROTEIN (DSRED) VARIANT Q66M