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(-) Description

Title :  CRYSTAL STRUCTURE OF RED FLUORESCENT PROTEIN FROM ZOANTHUS, ZRFP574, AT 2.4A RESOLUTION
 
Authors :  V. Pletnev, N. Pletneva, V. Martynov, T. Tikhonova, B. Popov, S. Pletnev
Date :  05 Jan 06  (Deposition) - 09 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (2x)
Biol. Unit 2:  B,C  (2x)
Keywords :  Red Fluorescent Protein, Button Polyp, Zoanthus Sp. , Crystal Structure, Chromophore, Beta-Can Fold, Beta Barrel, Tightly Packed Tetramer, Intersubunit Interface, Fluorescent Marker, Emission Maximum 574Nm, Zrfp574 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pletneva, S. Pletnev, T. Tikhonova, V. Popov, V. Martynov, V. Pletnev
Structure Of A Red Fluorescent Protein From Zoanthus, Zrfp574, Reveals A Novel Chromophore
Acta Crystallogr. , Sect. D V. 62 527 2006
PubMed-ID: 16627946  |  Reference-DOI: 10.1107/S0907444906007852
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN ZOANRFP
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: JM109DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ZOANTHUS SP.
    Organism Taxid: 105402

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A  D
Biological Unit 2 (2x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1SO49Ligand/IonSULFATE ION
2XYG4Mod. Amino Acid[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
2XYG4Mod. Amino Acid[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2XYG4Mod. Amino Acid[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:197 , LYS A:203 , ARG A:227 , SER A:228 , HOH A:568BINDING SITE FOR RESIDUE SO4 A 550
2AC2SOFTWAREASN A:36 , LYS A:39 , LYS A:41 , HOH A:670BINDING SITE FOR RESIDUE SO4 A 551
3AC3SOFTWARELYS A:172 , ARG A:206 , HOH A:584 , HOH A:635 , HOH A:647 , HOH A:673BINDING SITE FOR RESIDUE SO4 A 552
4AC4SOFTWARETRP B:197 , LYS B:203 , ARG B:227 , SER B:228 , HOH B:706 , HOH B:722BINDING SITE FOR RESIDUE SO4 B 650
5AC5SOFTWAREASN B:36 , LYS B:39 , LYS B:41BINDING SITE FOR RESIDUE SO4 B 651
6AC6SOFTWARETRP C:197 , LYS C:203 , ARG C:227 , SER C:228 , LEU C:230BINDING SITE FOR RESIDUE SO4 C 750
7AC7SOFTWAREASN C:36 , LYS C:39 , LYS C:41BINDING SITE FOR RESIDUE SO4 C 751
8AC8SOFTWARETHR C:142 , LYS C:172 , ARG C:206 , ASP C:208 , HOH C:864BINDING SITE FOR RESIDUE SO4 C 752
9AC9SOFTWAREPRO D:147 , TRP D:197 , LYS D:203 , ARG D:227 , SER D:228 , LEU D:230 , HOH D:873BINDING SITE FOR RESIDUE SO4 D 850

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2FL1)

(-) Cis Peptide Bonds  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2FL1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2FL1)

(-) Exons   (0, 0)

(no "Exon" information available for 2FL1)

(-) 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:226
 aligned with Q8T4U4_9CNID | Q8T4U4 from UniProtKB/TrEMBL  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8T4U4_9CNID     4 SKHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFDYGNRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
               SCOP domains d2fl1a_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2fl1A00 A:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeeee....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fl1 A   4 SAHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFd--NRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-XYG                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with Q8T4U4_9CNID | Q8T4U4 from UniProtKB/TrEMBL  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8T4U4_9CNID     4 SKHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFDYGNRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
               SCOP domains d2fl1b_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2fl1B00 B:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeeehhh.eeeeeeeeeee.....hhhhhh.eeee..eeeeeeee....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fl1 B   4 SAHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFd--NRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-XYG                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:226
 aligned with Q8T4U4_9CNID | Q8T4U4 from UniProtKB/TrEMBL  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8T4U4_9CNID     4 SKHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFDYGNRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
               SCOP domains d2fl1c_ C: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2fl1C00 C:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeeeehhhheeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fl1 C   4 SAHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFd--NRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-XYG                                                                                                                                                                 


Chain D from PDB  Type:PROTEIN  Length:226
 aligned with Q8T4U4_9CNID | Q8T4U4 from UniProtKB/TrEMBL  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
         Q8T4U4_9CNID     4 SKHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFDYGNRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
               SCOP domains d2fl1d_ D: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2fl1D00 D:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeee.....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeeee....eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fl1 D   4 SAHGLTDDMTMHFRMEGCVDGHKFVIEGNGNGNPFKGKQFINLCVIEGGPLPFSEDILSAAFd--NRLFTEYPEGIVDYFKNSCPAGYTWHRSFRFEDGAVCICSADITVNVRENCIYHESTFYGVNFPADGPVMKKMTTNWEPSCEKIIPINSQKILKGDVSMYLLLKDGGRYRCQFDTIYKAKTEPKEMPDWHFIQHKLNREDRSDAKNQKWQLIEHAIASRSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-XYG
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2FL1)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q8T4U4_9CNID | Q8T4U4)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

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(-) Related Entries Specified in the PDB File

1xa9 CRYSTAL STRUCTURE OF HOMOLOGOUS YELLOW FLUORESCENT PROTEIN ZYFP538.