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(-) Description

Title :  CRYSTAL STRUCTURE OF A DUF1285 FAMILY PROTEIN (SPO_0140) FROM SILICIBACTER POMEROYI DSS-3 AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  25 Sep 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. W. Han, C. Bakolitsa, M. D. Miller, A. Kumar, D. Carlton, R. J. Najmanovich, P. Abdubek, T. Astakhova, H. L. Axelrod, C. Chen, H. J. Chiu, T. Clayton, D. Das, M. C. Deller, L. Duan, D. Ernst, J. Feuerhelm, J. C. Grant, A. Grzechnik, L. Jaroszewski, K. K. Jin, H. A. Johnson, H. E. Klock, M. W. Knuth, P. Kozbial, S. S. Krishna, D. Marciano, D. Mcmullan, A. T. Morse, E. Nigoghossian, L. Okach, R. Reyes, C. L. Rife, N. Sefcovic, H. J. Tien, C. B. Trame, H. Van Den Bedem, D. Weekes, Q. Xu, K. O. Hodgson, J. Wooley, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structures Of The First Representatives Of Pfam Family Pf06938 (Duf1285) Reveal A New Fold With Repeated Structura Motifs And Possible Involvement In Signal Transduction.
Acta Crystallogr. , Sect. F V. 66 1218 2010
PubMed-ID: 20944214  |  Reference-DOI: 10.1107/S1744309109050416

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Atcc: 700808
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_165412.1, SPO0140
    Organism Scientific: SILICIBACTER POMEROYI DSS-3
    Organism Taxid: 246200
    Strain: DSS-3, DSM 15171

 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  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:22 , SER A:23BINDING SITE FOR RESIDUE GOL A 194

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RE3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser B:10 -Ala B:11

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2RE3)

(-) Exons   (0, 0)

(no "Exon" information available for 2RE3)

(-) 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:183
 aligned with Q5LWU5_RUEPO | Q5LWU5 from UniProtKB/TrEMBL  Length:193

    Alignment length:183
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189   
         Q5LWU5_RUEPO    10 SADGLLASARAIKSKGPAPVHLWNPPFNGDIDMRIARDGTWFYQGTPINRPAMVRLFSSILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRMAQDPATGEPAPYVHVRAGLEALIDRKSFYRLMDLGEIEDGWFGLWSSGSFFPLMTVEELER 192
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2re3A01 A:10-92 duf1285 like domain                                                2re3A02 A:93-162 duf1285 protein                                      -2re3A03 A:164-192             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......hhhhh...eeeeeeeee.....eee..ee..hhhhhhhhhh.eeee..eeeee....eeeeee....eeeeeeeee.hhhhheeeeee....eee......ee............eeeee..eeeeehhhhhhhhhh..eee..eeeeee..eeeeeeehhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2re3 A  10 SADGLLASARAIKSKGPAPVHLWNPPFNGDIDmRIARDGTWFYQGTPINRPAmVRLFSSILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRmAQDPATGEPAPYVHVRAGLEALIDRKSFYRLmDLGEIEDGWFGLWSSGSFFPLmTVEELER 192
                                    19        29        39  |     49        59  |     69        79        89        99       109       119       129 |     139       149       159   |   169       179     | 189   
                                                           42-MSE              62-MSE                                                              131-MSE                         163-MSE               185-MSE   


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with Q5LWU5_RUEPO | Q5LWU5 from UniProtKB/TrEMBL  Length:193

    Alignment length:184
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    
         Q5LWU5_RUEPO    10 SADGLLASARAIKSKGPAPVHLWNPPFNGDIDMRIARDGTWFYQGTPINRPAMVRLFSSILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRMAQDPATGEPAPYVHVRAGLEALIDRKSFYRLMDLGEIEDGWFGLWSSGSFFPLMTVEELERG 193
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2re3B01 B:10-92 duf1285 like domain                                                2re3B02 B:93-162 duf1285 protein                                      -2re3B03 B:164-193              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......hhhhh...eeeeeeeee.....eee..ee..hhhhhhhhhh.eeee..eeeee....eeeeee....eeeeeeeee.hhhhheeeeee....eee......eeeee......eeeeeeee..eeeeehhhhhhhhhh..eee..eeeeee..eeeeeeehhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2re3 B  10 SADGLLASARAIKSKGPAPVHLWNPPFNGDIDmRIARDGTWFYQGTPINRPAmVRLFSSILKREEDRFYLVTPVEKVGIRVDDAPFVAVDVEVAGQGRKQVLTFTTHVGDSAVAGEGNPIRmAQDPATGEPAPYVHVRAGLEALIDRKSFYRLmDLGEIEDGWFGLWSSGSFFPLmTVEELERG 193
                                    19        29        39  |     49        59  |     69        79        89        99       109       119       129 |     139       149       159   |   169       179     | 189    
                                                           42-MSE              62-MSE                                                              131-MSE                         163-MSE               185-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 2RE3)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2RE3)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5LWU5_RUEPO | Q5LWU5)
molecular function
    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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