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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A DOMAIN OF PROTEIN VP0806 (UNKNOWN FUNCTION) FROM VIBRIO PARAHAEMOLYTICUS RIMD 2210633
 
Authors :  K. Tan, R. Wu, J. Abdullah, L. Freeman, A. Joachimiak, Midwest Center Structural Genomics (Mcsg)
Date :  04 Sep 07  (Deposition) - 18 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Apc090868. 1, Protein Vp0806, Vibrio Parahaemolyticus Rimd 2210633, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tan, R. Wu, J. Abdullah, L. Freeman, A. Joachimiak
The Crystal Structure Of A Domain Of Protein Vp0806 (Unknow Function) From Vibrio Parahaemolyticus Rimd 2210633.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN VP0806
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPMCSG7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GeneVP0806
    Organism ScientificVIBRIO PARAHAEMOLYTICUS
    Organism Taxid223926
    StrainRIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:237 , ASN B:241 , LYS B:244 , TYR B:284 , HOH B:311BINDING SITE FOR RESIDUE ACT B 1
2AC2SOFTWARELEU A:118 , VAL A:121 , SER A:122 , ASP A:149 , ALA A:153 , HOH A:287BINDING SITE FOR RESIDUE MES A 4
3AC3SOFTWARELYS A:274 , ARG A:277 , GLN A:278 , TYR A:280 , SER A:281 , HOH A:289 , MES B:285BINDING SITE FOR RESIDUE EDO A 2
4AC4SOFTWAREHIS A:193 , ALA A:196 , GLN A:228 , VAL A:229 , MES B:2BINDING SITE FOR RESIDUE EDO A 3
5AC5SOFTWAREEDO A:2 , LYS A:274 , TYR A:280 , LEU B:192 , HIS B:193BINDING SITE FOR RESIDUE MES B 285
6AC6SOFTWAREEDO A:3 , HIS A:193 , LYS B:274 , TYR B:280BINDING SITE FOR RESIDUE MES B 2
7AC7SOFTWARELEU B:118 , LYS B:119 , SER B:122 , ASP B:149BINDING SITE FOR RESIDUE MES B 3
8AC8SOFTWAREVAL B:245 , ASN B:246 , LEU B:247BINDING SITE FOR RESIDUE EDO B 286

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R5S)

(-) Exons   (0, 0)

(no "Exon" information available for 2R5S)

(-) 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:171
 aligned with Q87RI8_VIBPA | Q87RI8 from UniProtKB/TrEMBL  Length:284

    Alignment length:171
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 
         Q87RI8_VIBPA   114 DEQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQLYSILY 284
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r5sA01 A:114-196  [code=1.25.40.10, no name defined]                              2r5sA02 A:197-284  [code=1.25.40.10, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5s A 114 DEQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFmDILSALGQGNAIASKYRRQLYSILY 284
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253     | 263       273       283 
                                                                                                                                                                           259-MSE                     

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with Q87RI8_VIBPA | Q87RI8 from UniProtKB/TrEMBL  Length:284

    Alignment length:171
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283 
         Q87RI8_VIBPA   114 DEQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFMDILSALGQGNAIASKYRRQLYSILY 284
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2r5sB01 B:114-196  [code=1.25.40.10, no name defined]                              2r5sB02 B:197-284  [code=1.25.40.10, no name defined]                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r5s B 114 DEQLLKQVSELLQQGEHAQALNVIQTLSDELQSRGDVKLAKADCLLETKQFELAQELLATIPLEYQDNSYKSLIAKLELHQQAAESPELKRLEQELAANPDNFELACELAVQYNQVGRDEEALELLWNILKVNLGAQDGEVKKTFmDILSALGQGNAIASKYRRQLYSILY 284
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253     | 263       273       283 
                                                                                                                                                                           259-MSE                     

   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  (0, 0)

(no "SCOP Domain" information available for 2R5S)

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2R5S)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q87RI8_VIBPA | Q87RI8)
molecular function
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0006662    glycerol ether metabolic process    The chemical reactions and pathways involving glycerol ethers, any anhydride formed between two organic hydroxy compounds, one of which is glycerol.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005623    cell    The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

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