4RN7

The crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.717 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The crystal structure of N-acetylmuramoyl-L-alanine amidase from Clostridium difficile 630

Tan, K.Mulligan, R.Kwon, K.Anderson, W.F.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylmuramoyl-L-alanine amidase
A
188Peptoclostridium difficile (strain 630)Mutation(s): 0 
EC: 3.5.1.28
Find proteins for Q183J9 (Peptoclostridium difficile (strain 630))
Go to UniProtKB:  Q183J9
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 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 = 66.407α = 90.00
b = 66.407β = 90.00
c = 96.200γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
SBC-Collectdata collection
HKL-3000data scaling
DMphasing
DMmodel building
PHENIXrefinement
HKL-3000data reduction
SHELXDphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-05
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Refinement description