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(-) Description

Title :  THE CRYSTAL STRUCTURE OF GENE PRODUCT VP1028 FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  R. Zhang, M. Zhou, S. Moy, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  21 Dec 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Vibrio Parahaemolyticus, Unknown Function, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Zhang, M. Zhou, S. Moy, A. Joachimiak
The Crystal Structure Of Gene Product Vp1028 From Vibrio Parahaemolyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN VP1028
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-105
    Gene: VP1028
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 223926
    Strain: RIMD 2210633

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE6Mod. Amino AcidSELENOMETHIONINE
3SO49Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:7 , HOH A:414 , PRO B:4 , LYS B:7BINDING SITE FOR RESIDUE MG B 301
02AC2SOFTWAREARG A:48 , GLN A:51BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREASN B:42 , GLN B:44 , HIS B:46 , TYR B:65 , HOH B:409 , HOH B:420 , HOH B:488BINDING SITE FOR RESIDUE SO4 B 401
04AC4SOFTWAREARG B:48 , ASP B:50 , GLN B:51BINDING SITE FOR RESIDUE SO4 B 402
05AC5SOFTWARELYS B:69 , ARG B:70BINDING SITE FOR RESIDUE SO4 B 403
06AC6SOFTWARELYS A:68 , LYS A:69 , ARG A:70 , HOH A:499BINDING SITE FOR RESIDUE SO4 A 404
07AC7SOFTWAREHIS A:46 , TYR A:65 , HOH A:411 , HOH A:425 , HOH A:473 , HOH A:513BINDING SITE FOR RESIDUE SO4 A 405
08AC8SOFTWAREGLY A:17 , THR A:18 , THR B:59 , HOH B:449 , HOH B:492BINDING SITE FOR RESIDUE SO4 B 406
09AC9SOFTWARELYS B:68 , GLY B:71 , LYS B:98 , HOH B:441BINDING SITE FOR RESIDUE SO4 B 407
10BC1SOFTWAREARG B:48 , LYS B:77 , TYR B:78 , HOH B:416 , HOH B:422BINDING SITE FOR RESIDUE SO4 B 408
11BC2SOFTWARELYS A:7 , LYS A:11 , HOH A:410 , HOH A:445 , VAL B:41 , ASN B:42 , ASN B:43BINDING SITE FOR RESIDUE SO4 A 409

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OD0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OD0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OD0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OD0)

(-) Exons   (0, 0)

(no "Exon" information available for 2OD0)

(-) 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:103
 aligned with Q87QX1_VIBPA | Q87QX1 from UniProtKB/TrEMBL  Length:196

    Alignment length:103
                                    12        22        32        42        52        62        72        82        92       102   
         Q87QX1_VIBPA     3 KPILKDSMKLFEALGTIKSRSMFGGFGLFADETMFALVVNNQLHIRADQQTSSDFETQGLKPYVYKKRGFPVVTKYYAISSELWESSDRLIEVAKKSLENAKL 105
               SCOP domains d2od0a1 A:3-105 Hypothetical protein VP1028                                                             SCOP domains
               CATH domains 2od0A00 A:3-105 YgaC/TfoX-N like chaperone                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeee..eeeeee..eeeeeee..eeeee.hhhhhhhhhhh.....eeee..eeee..eee.hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2od0 A   3 KPILKDSmKLFEALGTIKSRSmFGGFGLFADETmFALVVNNQLHIRADQQTSSDFETQGLKPYVYKKRGFPVVTKYYAISSELWESSDRLIEVAKKSLENAKL 105
                                   |12        22 |      32   |    42        52        62        72        82        92       102   
                                  10-MSE        24-MSE      36-MSE                                                                 


Chain B from PDB  Type:PROTEIN  Length:102
 aligned with Q87QX1_VIBPA | Q87QX1 from UniProtKB/TrEMBL  Length:196

    Alignment length:102
                                    12        22        32        42        52        62        72        82        92       102  
         Q87QX1_VIBPA     3 KPILKDSMKLFEALGTIKSRSMFGGFGLFADETMFALVVNNQLHIRADQQTSSDFETQGLKPYVYKKRGFPVVTKYYAISSELWESSDRLIEVAKKSLENAK 104
               SCOP domains d2od0b_ B: Hypothetical protein VP1028                                                                 SCOP domains
               CATH domains 2od0B00 B:3-104 YgaC/TfoX-N like chaperone                                                             CATH domains
           Pfam domains (1) ------TfoX_N-2od0B01 B:9-104                                                                           Pfam domains (1)
           Pfam domains (2) ------TfoX_N-2od0B02 B:9-104                                                                           Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhh.eeeeee..eeeeee..eeeeeee..eeeee.hhhhhhhhhhh.....eeee..eeee..eee.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 2od0 B   3 KPILKDSmKLFEALGTIKSRSmFGGFGLFADETmFALVVNNQLHIRADQQTSSDFETQGLKPYVYKKRGFPVVTKYYAISSELWESSDRLIEVAKKSLENAK 104
                                   |12        22 |      32   |    42        52        62        72        82        92       102  
                                  10-MSE        24-MSE      36-MSE
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TfoX_N] (1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2OD0)

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