4RN7

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

PDB DOI: https://doi.org/10.2210/pdb4RN7/pdb

Classification: HYDROLASE
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-23 Released: 2014-11-05
Deposition Author(s): Tan, K., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.215
R-Value Work: 0.195
R-Value Observed: 0.196

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.

Macromolecule Content

Total Structure Weight: 21.61 kDa
Atom Count: 1,624
Modelled Residue Count: 186
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase	A	188	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_27610 EC: 3.5.1.28
UniProt
Find proteins for Q183J9 (Clostridioides difficile (strain 630)) Explore Q183J9 Go to UniProtKB: Q183J9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q183J9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.215
R-Value Work: 0.195
R-Value Observed: 0.196
Space Group: P 3₂ 2 1
Diffraction Data: https://doi.org/10.18430/m34rn7

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.407	α = 90
b = 66.407	β = 90
c = 96.2	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing