2QTP

Crystal structure of a duf1185 family protein (spo0826) from silicibacter pomeroyi dss-3 at 2.10 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism.

Bakolitsa, C.Kumar, A.Jin, K.K.McMullan, D.Krishna, S.S.Miller, M.D.Abdubek, P.Acosta, C.Astakhova, T.Axelrod, H.L.Burra, P.Carlton, D.Chen, C.Chiu, H.J.Clayton, T.Das, D.Deller, M.C.Duan, L.Elias, Y.Ellrott, K.Ernst, D.Farr, C.L.Feuerhelm, J.Grant, J.C.Grzechnik, A.Grzechnik, S.K.Han, G.W.Jaroszewski, L.Johnson, H.A.Klock, H.E.Knuth, M.W.Kozbial, P.Marciano, D.Morse, A.T.Murphy, K.D.Nigoghossian, E.Nopakun, A.Okach, L.Paulsen, J.Puckett, C.Reyes, R.Rife, C.L.Sefcovic, N.Tien, H.J.Trame, C.B.Trout, C.V.van den Bedem, H.Weekes, D.White, A.Xu, Q.Hodgson, K.O.Wooley, J.Elsliger, M.A.Deacon, A.M.Godzik, A.Lesley, S.A.Wilson, I.A.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1182-1189

  • DOI: 10.1107/S1744309109050647
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of th ...

    The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis.


    Organizational Affiliation

    Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized proteinA194Ruegeria pomeroyi DSS-3Mutation(s): 0 
Gene Names: YP_166079.1SPO0826
Find proteins for Q5LV76 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3))
Explore Q5LV76 
Go to UniProtKB:  Q5LV76
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.73α = 90
b = 94.73β = 90
c = 47.15γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
SHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-08-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-10-24
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description