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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE HOST-NUCLEASE INHIBITOR PROTEIN GAM FROM DESULFOVIBRIO VULGARIS
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, F. Zhang, R. Romero, D. Smith, S. Was J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  07 Mar 07  (Deposition) - 27 Mar 07  (Release) - 24 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Structural Genomics, Unknown Function, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, F. Zhang, R. Romero, D. Smith, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Host-Nuclease Inhibitor Protein Gam From Desulfovibrio Vulgaris
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOST-NUCLEASE INHIBITOR PROTEIN GAM, PUTATIVE
    Atcc: 29579
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Gene: DVU_1136
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 881
    Strain: HILDENBOROUGH, NCIMB 8303

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2P2U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P2U)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:150
 aligned with Q72CZ5_DESVH | Q72CZ5 from UniProtKB/TrEMBL  Length:170

    Alignment length:153
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158   
         Q72CZ5_DESVH     9 VIVADIRQAEGALAEIATIDRKVGEIEAQMNEAIDAAKARASQKSAPLLARRKELEDGVATFATLNKTEMFKDRKSLDLGFGTIGFRLSTQIVQMSKITKDMTLERLRQFGISEGIRIKEDVNKEAMQGWPDERLEMVGLKRRTTDAFYIEIN 161
               SCOP domains d2p2ua1 A:9-161 Host-nuclease inhibitor protein Gam, putative                                                                                             SCOP domains
               CATH domains 2p2uA01 A:9-79  [code=1.20.5.170, no name defined]                     ---------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---........................hhhhhhhhhhhh............hhhhhh..hhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p2u A   9 VIVADIRQAEGALAEIATIDRKVGEIEAQmNEAIDAAKARASQKSAPLLARRKELEDGVATFATLNKTEmF---KSLDLGFGTIGFRLSTQIVQmSKITKDmTLERLRQFGISEGIRIKEDVNKEAmQGWPDERLEmVGLKRRTTDAFYIEIN 161
                                    18        28        38        48        58        68        78|   |   88        98    |  108 |     118       128      |138      |148       158   
                                                        38-MSE                                  78-MSE3                 103-MSE  |                      135-MSE   145-MSE            
                                                                                                 79                            110-MSE                                               


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with Q72CZ5_DESVH | Q72CZ5 from UniProtKB/TrEMBL  Length:170

    Alignment length:157
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       
         Q72CZ5_DESVH     9 VIVADIRQAEGALAEIATIDRKVGEIEAQMNEAIDAAKARASQKSAPLLARRKELEDGVATFATLNKTEMFKDRKSLDLGFGTIGFRLSTQIVQMSKITKDMTLERLRQFGISEGIRIKEDVNKEAMQGWPDERLEMVGLKRRTTDAFYIEINREEV 165
               SCOP domains d2p2ub_ B: Host-nuclease inhibitor protein Gam, putative                                                                                                      SCOP domains
               CATH domains 2p2uB01 B:9-79  [code=1.20.5.170, no name defined]                     -------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Phage_Mu_Gam-2p2uB01 B:13-160                                                                                                                       ----- Pfam domains (1)
           Pfam domains (2) ----Phage_Mu_Gam-2p2uB02 B:13-160                                                                                                                       ----- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----.ee....ee..............hhhhhhhhhhhhhhhhhh......hhhhhh..hhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p2u B   9 VIVADIRQAEGALAEIATIDRKVGEIEAQmNEAIDAAKARASQKSAPLLARRKELEDGVATFATLNKTEmF----SLDLGFGTIGFRLSTQIVQmSKITKDmTLERLRQFGISEGIRIKEDVNKEAmQGWPDERLEmVGLKRRTTDAFYIEINREEV 165
                                    18        28        38        48        58        68        78|    |  88        98    |  108 |     118       128      |138      |148       158       
                                                        38-MSE                                  78-MSE84                103-MSE  |                      135-MSE   145-MSE                
                                                                                                 79                            110-MSE
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Phage_Mu_Gam] (1)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q72CZ5_DESVH | Q72CZ5)
molecular function
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
biological process
    GO:0042262    DNA protection    Any process in which DNA is protected from damage by, for example, oxidative stress.

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