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(-) Description

Title :  PUTATIVE HOPJ TYPE III EFFECTOR PROTEIN FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  Y. Kim, C. Chang, L. Volkart, J. Abdullah, A. Joachimiak, Midwest Cent Structural Genomics (Mcsg)
Date :  13 Jul 07  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Alpha-Beta Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, C. Chang, L. Volkart, J. Abdullah, A. Joachimiak
Crystal Structure Of Putative Hopj Type Iii Effector Protei From Vibrio Parahaemolyticus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE HOPJ TYPE III EFFECTOR PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VPA0580
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 223926
    Strain: RIMD 2210633
    Synonym: UNCHARACTERIZED PROTEIN VPA0580

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K1Ligand/IonPOTASSIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA1Ligand/IonSODIUM ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE8Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (3, 20)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE16Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
5TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:109 , GLU A:110 , ILE A:112 , ASN B:70 , HOH B:229 , HOH B:251BINDING SITE FOR RESIDUE K A 201
2AC2SOFTWARELEU A:69 , TRP B:109 , GLU B:110 , ILE B:112 , HOH B:233 , HOH B:241BINDING SITE FOR RESIDUE NA B 202
3AC3SOFTWAREASN A:57 , ASP A:97 , HIS A:98 , ASN B:57 , ASP B:97 , HIS B:98 , GLN B:99 , HOH B:218 , HOH B:226 , HOH B:237 , HOH B:255BINDING SITE FOR RESIDUE TRS B 203
4AC4SOFTWAREALA A:65 , LEU A:68 , LEU A:69 , PHE A:114 , SER A:117 , ALA A:118 , LEU A:119 , HOH A:258BINDING SITE FOR RESIDUE GOL A 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QM2)

(-) Exons   (0, 0)

(no "Exon" information available for 2QM2)

(-) 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:118
 aligned with Q87IM6_VIBPA | Q87IM6 from UniProtKB/TrEMBL  Length:122

    Alignment length:118
                                    14        24        34        44        54        64        74        84        94       104       114        
         Q87IM6_VIBPA     5 FGMKMELQQFLDALASSPEKIEFETTMAVIEDNYDFTPAAFTNGNTQNDANENNGSCKIFAFGLLNALDKEATLACFGRFYREDVLLHPENNDHQNIRNFMVTGWEGIQFETSALTAK 122
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qm2A00 A:5-122 vpa0580 domain like                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee..eee....hhhhhhhhhhhhhh..hhhhhhhh.hhhhhh..........hhhhhhhhhhh...eee....eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm2 A   5 FGmKmELQQFLDALASSPEKIEFETTmAVIEDNYDFTPAAFTNGNTQNDANENNGSCKIFAFGLLNALDKEATLACFGRFYREDVLLHPENNDHQNIRNFmVTGWEGIQFETSALTAK 122
                              | |   14        24      | 34        44        54        64        74        84        94       104|      114        
                              | |                    31-MSE                                                                   105-MSE             
                              7-MSE                                                                                                               
                                9-MSE                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with Q87IM6_VIBPA | Q87IM6 from UniProtKB/TrEMBL  Length:122

    Alignment length:116
                                    16        26        36        46        56        66        76        86        96       106       116      
         Q87IM6_VIBPA     7 MKMELQQFLDALASSPEKIEFETTMAVIEDNYDFTPAAFTNGNTQNDANENNGSCKIFAFGLLNALDKEATLACFGRFYREDVLLHPENNDHQNIRNFMVTGWEGIQFETSALTAK 122
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -2qm2B00 B:8-122 vpa0580 domain like                                                                                 CATH domains
           Pfam domains (1) --HopJ-2qm2B01 B:9-119                                                                                           --- Pfam domains (1)
           Pfam domains (2) --HopJ-2qm2B02 B:9-119                                                                                           --- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhheee....eee..eee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhheee....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2qm2 B   7 mKmELQQFLDALASSPEKIEFETTmAVIEDNYDFTPAAFTNGNTQNDANENNGSCKIFAFGLLNALDKEATLACFGRFYREDVLLHPENNDHQNIRNFmVTGWEGIQFETSALTAK 122
                            | |     16        26    |   36        46        56        66        76        86        96       106       116      
                            7-MSE                  31-MSE                                                                   105-MSE             
                              9-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  (0, 0)

(no "SCOP Domain" information available for 2QM2)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: HopJ] (2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2QM2)

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 Related Entries

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UniProtKB/TrEMBL
        Q87IM6_VIBPA | Q87IM6: 2qhq

(-) Related Entries Specified in the PDB File

2qhq LYSYL METHYLATED PROTEIN