7V6U | pdb_00007v6u

Crystal structure of bacterial peptidase

• PDB DOI: https://doi.org/10.2210/pdb7V6U/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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of bacterial DD-endopeptidase

Lee, W.C., Lee, J., Kim, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.46 kDa 
• Atom Count: 2,068 
• Modeled Residue Count: 253 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

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 (PDB Primary Data), 3.4 (UniProt)
UniProt
Find proteins for P0AFV4 (Escherichia coli (strain K12)) Explore P0AFV4  Go to UniProtKB:  P0AFV4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	C [auth A], E [auth B]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
EDO	D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.871	α = 90
b = 76.825	β = 134.66
c = 58.207	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Kim, Y., Lee, W.C.

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

Revision History  

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