3LK7

The Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate (MurD) ligase from Streptococcus agalactiae to 1.5A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Crystal Structure of UDP-N-acetylmuramoylalanine-D-glutamate (MurD) ligase from Streptococcus agalactiae to 1.5A

Stein, A.J.Sather, A.Shakelford, G.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
UDP-N-acetylmuramoylalanine--D-glutamate ligase
A
451Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)Gene Names: murD
EC: 6.3.2.9
Find proteins for Q8E186 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R))
Go to UniProtKB:  Q8E186
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 161.539α = 90.00
b = 65.045β = 107.52
c = 52.889γ = 90.00
Software Package:
Software NamePurpose
SHELXphasing
Cootmodel building
DENZOdata reduction
PDB_EXTRACTdata extraction
HKL-3000data reduction
SCALEPACKdata scaling
HKL-3000data scaling
REFMACrefinement
SBC-Collectdata collection
DMphasing
MLPHAREphasing
ARP/wARPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description