3BYQ

Crystal structure of a duf1185 family protein (bb2672) from bordetella bronchiseptica rb50 at 1.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.138 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 66: 1182-1189

  • DOI: 10.1107/S1744309109050647
  • Primary Citation of Related Structures:  2QTP

  • 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 protein DUF1185
A, B, C
193Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)N/A
Find proteins for A0A0H3LTD0 (Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50))
Go to UniProtKB:  A0A0H3LTD0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, C
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 96.542α = 90.00
b = 133.127β = 90.00
c = 92.544γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHENIXrefinement
SHELXDphasing
MAR345data collection
MOSFLMdata reduction
SHELXphasing
MolProbitymodel building
SCALAdata scaling
autoSHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Author supporting evidence, Refinement description