3TX8

Crystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.972 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

Brunger, A.T.Das, D.Deacon, A.M.Grant, J.Terwilliger, T.C.Read, R.J.Adams, P.D.Levitt, M.Schroder, G.F.

(2012) Acta Crystallogr.,Sect.D 68: 391-403

  • DOI: 10.1107/S090744491104978X

  • PubMed Abstract: 
  • Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a ...

    Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.


    Organizational Affiliation

    Department of Molecular and Cellular Physiology, Stanford University, USA. brunger@stanford.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Succinyl-diaminopimelate desuccinylase
A
369Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)Mutation(s): 0 
Gene Names: dapE
EC: 3.5.1.18
Find proteins for Q59284 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025))
Go to UniProtKB:  Q59284
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 82.901α = 90.00
b = 82.901β = 90.00
c = 364.175γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction
CNSphasing
MolProbitymodel building
PDB_EXTRACTdata extraction
PHASERphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2012-10-10
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description