7V6S

Crystal structure of bacterial peptidase

PDB DOI: https://doi.org/10.2210/pdb7V6S/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-08-20 Released: 2022-08-24
Deposition Author(s): Kim, Y., Lee, W.C.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.249
R-Value Work: 0.211
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

The crystal structure fre

Lee, W.C., Lee, J., Kim, Y.

To be published.

Macromolecule Content

Total Structure Weight: 30.07 kDa
Atom Count: 2,021
Modelled Residue Count: 248
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Murein DD-endopeptidase MepS/Murein LD-carboxypeptidase	A, B	132	Escherichia coli K-12	Mutation(s): 1 Gene Names: mepS, spr, yeiV, b2175, JW2163 EC: 3.4.17.13
UniProt
Find proteins for P0AFV4 (Escherichia coli (strain K12)) Explore P0AFV4 Go to UniProtKB: P0AFV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0AFV4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.88 Å
R-Value Free: 0.249
R-Value Work: 0.211
R-Value Observed: 0.215
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.835	α = 90
b = 59.835	β = 90
c = 133.777	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.