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(-) Description

Title :  CRYSTAL STRUCTURE OF A DUF1989 FAMILY PROTEIN (SPO0365) FROM SILICIBACTER POMEROYI DSS-3 AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Jun 08  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Protein Of Unknown Function (Duf1989) (Yp_165628. 1) From Silicibacter Pomeroyi Dss-3 At 1. 60 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN DUF1989
    Atcc: 700808
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Vector Type: PLASMID
    Gene: YP_165628.1, SPO0365
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 246200
    Strain: DSS-3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE11Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:150 , CYS A:167 , CYS A:237BINDING SITE FOR RESIDUE ZN A 286
2AC2SOFTWARECYS B:150 , CYS B:167 , CYS B:237BINDING SITE FOR RESIDUE ZN B 286
3AC3SOFTWARETYR A:24 , LYS A:97 , ALA A:100 , THR B:148 , ARG B:149 , TYR B:209BINDING SITE FOR RESIDUE SO4 B 287
4AC4SOFTWAREHIS A:164 , GLY B:161BINDING SITE FOR RESIDUE CL B 288
5AC5SOFTWARETHR A:148 , ARG A:149 , LYS B:97BINDING SITE FOR RESIDUE CL A 287
6AC6SOFTWAREARG B:55 , CYS B:253BINDING SITE FOR RESIDUE CL B 289
7AC7SOFTWAREGLY A:161 , HIS B:164BINDING SITE FOR RESIDUE CL A 288
8AC8SOFTWAREPRO A:218 , GLY A:219 , ASP A:220BINDING SITE FOR RESIDUE GOL A 289

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DI4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:116 -Pro A:117
2Leu B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DI4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DI4)

(-) Exons   (0, 0)

(no "Exon" information available for 3DI4)

(-) 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:281
 aligned with Q5LXE3_RUEPO | Q5LXE3 from UniProtKB/TrEMBL  Length:285

    Alignment length:286
                             1                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279      
         Q5LXE3_RUEPO     - -MTDAPADAPLDADARRAVKPVICYPNDSLPRPDLALYRAARASARKTGEVLVPPREGRCFEVKAGQFFRISSVEGPQVGDLNLHNLHDLTERFFSGKTRALHGTHVTTGERLWSNLPYLRPMATIIEDTLGWYGIDQYGGSVHDVIGTRCDPYTGNLLAGGHYHHCCHSNLTRALADHTGLPLHEAEMLVHDVLNVFMCTGFTRDTGQYFMKASPVRPGDYLEFFAEIDLLGNLSACPGGDCSSEHSSDTASCHPLLVEIFAPAEGMLGDWPSPSVNGYDRSHGR 285
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhh..ee..hhhhh...hhhhhhhhhhh.eeeeeeee....eeeeee....eeeeee......eeeeeee..eeeee.hhhhhhhhhh.......eee.......eeeeeeee............eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhh.....eeeeeeeee......eeee........eeeeee...eeeeeee.........-----.....eeeeeee....................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3di4 A   0 GmTDAPADAPLDADARRAVKPVICYPNDSLPRPDLALYRAARASARKTGEVLVPPREGRCFEVKAGQFFRISSVEGPQVGDLNLHNLHDLTERFFSGKTRALHGTHVTTGERLWSNLPYLRPmATIIEDTLGWYGIDQYGGSVHDVIGTRCDPYTGNLLAGGHYHHCCHSNLTRALADHTGLPLHEAEmLVHDVLNVFmCTGFTRDTGQYFmKASPVRPGDYLEFFAEIDLLGNLSACPGGDCSSE-----ASCHPLLVEIFAPAEGmLGDWPSPSVNGYDRSHGR 285
                             |       9        19        29        39        49        59        69        79        89        99       109       119  |    129       139       149       159       169       179       189       199       209 |     219       229       239     |   - |     259       269       279      
                             |                                                                                                                      122-MSE                                                           188-MSE   198-MSE      211-MSE                           245   251             267-MSE              
                             1-MSE                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:274
 aligned with Q5LXE3_RUEPO | Q5LXE3 from UniProtKB/TrEMBL  Length:285

    Alignment length:279
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276         
         Q5LXE3_RUEPO     7 DAPLDADARRAVKPVICYPNDSLPRPDLALYRAARASARKTGEVLVPPREGRCFEVKAGQFFRISSVEGPQVGDLNLHNLHDLTERFFSGKTRALHGTHVTTGERLWSNLPYLRPMATIIEDTLGWYGIDQYGGSVHDVIGTRCDPYTGNLLAGGHYHHCCHSNLTRALADHTGLPLHEAEMLVHDVLNVFMCTGFTRDTGQYFMKASPVRPGDYLEFFAEIDLLGNLSACPGGDCSSEHSSDTASCHPLLVEIFAPAEGMLGDWPSPSVNGYDRSHGR 285
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh..ee..hhhhh...hhhhhhhhhhh.eeeeeeee....eeeeee....eeeeee......eeeeeee..eeeee.hhhhhhhhhh.......eee.......eeeeeeee............eeee......hhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhh...eeeeeeeee......eeee........eeeeee...eeeeeee.........-----.....eeeeeee....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3di4 B   7 DAPLDADARRAVKPVICYPNDSLPRPDLALYRAARASARKTGEVLVPPREGRCFEVKAGQFFRISSVEGPQVGDLNLHNLHDLTERFFSGKTRALHGTHVTTGERLWSNLPYLRPmATIIEDTLGWYGIDQYGGSVHDVIGTRCDPYTGNLLAGGHYHHCCHSNLTRALADHTGLPLHEAEmLVHDVLNVFmCTGFTRDTGQYFmKASPVRPGDYLEFFAEIDLLGNLSACPGGDCSSE-----ASCHPLLVEIFAPAEGmLGDWPSPSVNGYDRSHGR 285
                                    16        26        36        46        56        66        76        86        96       106       116     | 126       136       146       156       166       176       186 |     196 |     206    |  216       226       236        |-    |  256       266|      276         
                                                                                                                                             122-MSE                                                           188-MSE   198-MSE      211-MSE                           245   251             267-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  (0, 0)

(no "SCOP Domain" information available for 3DI4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DI4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DI4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5LXE3_RUEPO | Q5LXE3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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