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(-) Description

Title :  THE 2.1A CRYSTAL STRUCTURE OF THE FAR-RED FLUORESCENT PROTEIN HCRED: INHERENT CONFORMATIONAL FLEXIBILITY OF THE CHROMOPHORE
 
Authors :  P. G. Wilmann, J. Petersen, A. Pettikiriarachchi, A. M. Buckle, R. J. Devenish, M. Prescott, J. Rossjohn
Date :  28 Feb 05  (Deposition) - 17 May 05  (Release) - 30 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. G. Wilmann, J. Petersen, A. Pettikiriarachchi, A. M. Buckle, S. C. Smith, S. Olsen, M. A. Perugini, R. J. Devenish, M. Prescott, J. Rossjohn
The 2. 1A Crystal Structure Of The Far-Red Fluorescent Protein Hcred: Inherent Conformational Flexibility Of The Chromophore
J. Mol. Biol. V. 349 223 2005
PubMed-ID: 15876379  |  Reference-DOI: 10.1016/J.JMB.2005.03.020
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GFP-LIKE NON-FLUORESCENT CHROMOPROTEIN
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPQE10
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonLEATHERY SEA ANEMONE
    Organism ScientificHETERACTIS CRISPA
    Organism Taxid175771
    SynonymHCRED

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1CRU4Mod. Amino Acid4-[(4Z)-1-(CARBOXYMETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-2-YL]-4-IMINOBUTANOIC ACID
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:99 , GLY B:100 , ASN B:126 , GLU C:98 , TYR D:175BINDING SITE FOR RESIDUE PEG B 1001
2AC2SOFTWAREGLU C:92 , THR C:94 , HIS C:106 , HOH C:1049BINDING SITE FOR RESIDUE PEG C 1002

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:50 -Pro A:51
2Phe A:85 -Pro A:86
3Ala B:50 -Pro B:51
4Phe B:85 -Pro B:86
5Ala C:50 -Pro C:51
6Phe C:85 -Pro C:86
7Ala D:50 -Pro D:51
8Phe D:85 -Pro D:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YZW)

(-) 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:221
 aligned with NFCP_HETCR | Q95W85 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           NFCP_HETCR     3 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFTGTQSMRIHVTEGAPLPFAFDILAPCCEYGSRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVLGTNFPADGPVMKNKSGGWEPCTEVVYPENGVLCGRNVMALKVGDRRLICHLYTSYRSKKAVRALTMPGFHFTDIRLQMPRKKKDEYFELYEASVARYSDLPEK 225
               SCOP domains d1yzwa_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yzw A   4 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFAGTQSMRIHVTEGAPLPFAFDILAPCCe--SRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVHGTNFPADGPVMKNKSGGWEPSTEVVYPENGVLCGRNVMALKVGDRHLICHHYTSYRSKKAVRALTMPGFHFTDIRLQMLRKKKDEYFELYEASVARYSDLPEK 226
                                    13        23        33        43        53        63|  |    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                                                                       64-CRU                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:221
 aligned with NFCP_HETCR | Q95W85 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           NFCP_HETCR     3 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFTGTQSMRIHVTEGAPLPFAFDILAPCCEYGSRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVLGTNFPADGPVMKNKSGGWEPCTEVVYPENGVLCGRNVMALKVGDRRLICHLYTSYRSKKAVRALTMPGFHFTDIRLQMPRKKKDEYFELYEASVARYSDLPEK 225
               SCOP domains d1yzwb_ B: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yzw B   4 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFAGTQSMRIHVTEGAPLPFAFDILAPCCe--SRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVHGTNFPADGPVMKNKSGGWEPSTEVVYPENGVLCGRNVMALKVGDRHLICHHYTSYRSKKAVRALTMPGFHFTDIRLQMLRKKKDEYFELYEASVARYSDLPEK 226
                                    13        23        33        43        53        63|  |    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                                                                       64-CRU                                                                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:221
 aligned with NFCP_HETCR | Q95W85 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           NFCP_HETCR     3 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFTGTQSMRIHVTEGAPLPFAFDILAPCCEYGSRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVLGTNFPADGPVMKNKSGGWEPCTEVVYPENGVLCGRNVMALKVGDRRLICHLYTSYRSKKAVRALTMPGFHFTDIRLQMPRKKKDEYFELYEASVARYSDLPEK 225
               SCOP domains d1yzwc_ C: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee.....hhhhhh.......eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yzw C   4 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFAGTQSMRIHVTEGAPLPFAFDILAPCCe--SRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVHGTNFPADGPVMKNKSGGWEPSTEVVYPENGVLCGRNVMALKVGDRHLICHHYTSYRSKKAVRALTMPGFHFTDIRLQMLRKKKDEYFELYEASVARYSDLPEK 226
                                    13        23        33        43        53        63|  |    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                                                                       64-CRU                                                                                                                                                              

Chain D from PDB  Type:PROTEIN  Length:221
 aligned with NFCP_HETCR | Q95W85 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           NFCP_HETCR     3 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFTGTQSMRIHVTEGAPLPFAFDILAPCCEYGSRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVLGTNFPADGPVMKNKSGGWEPCTEVVYPENGVLCGRNVMALKVGDRRLICHLYTSYRSKKAVRALTMPGFHFTDIRLQMPRKKKDEYFELYEASVARYSDLPEK 225
               SCOP domains d1yzwd_ D: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GFP-1yzwD01 D:4-221                                                                                                                                                                                                       ----- Pfam domains (1)
           Pfam domains (2) GFP-1yzwD02 D:4-221                                                                                                                                                                                                       ----- Pfam domains (2)
           Pfam domains (3) GFP-1yzwD03 D:4-221                                                                                                                                                                                                       ----- Pfam domains (3)
           Pfam domains (4) GFP-1yzwD04 D:4-221                                                                                                                                                                                                       ----- Pfam domains (4)
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.......hhhhh...eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee..................eeeeeeee..eeeeeeeeeeee..eeeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee...eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yzw D   4 GLLKESMRIKMYMEGTVNGHYFKCEGEGDGNPFAGTQSMRIHVTEGAPLPFAFDILAPCCe--SRTFVHHTAEIPDFFKQSFPEGFTWERTTTYEDGGILTAHQDTSLEGNCLIYKVKVHGTNFPADGPVMKNKSGGWEPSTEVVYPENGVLCGRNVMALKVGDRHLICHHYTSYRSKKAVRALTMPGFHFTDIRLQMLRKKKDEYFELYEASVARYSDLPEK 226
                                    13        23        33        43        53        63|  |    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223   
                                                                                       64-CRU                                                                                                                                                              

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YZW)

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (NFCP_HETCR | Q95W85)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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