8Z4H | pdb_00008z4h

Pseudomurein Endoisopeptidase PeiR

• PDB DOI: https://doi.org/10.2210/pdb8Z4H/pdb

• Classification: HYDROLASE
• Organism(s): Methanobrevibacter ruminantium M1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-17 Released: 2025-04-23 
• Deposition Author(s): Guo, L.Z., Wang, S.X., Bai, L.p.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.285 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: in silico

Literature

Pseudomurein Endoisopeptidase PeiR

Guo, L.Z., Wang, S.X., Bai, L.p.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 105.09 kDa 
• Atom Count: 7,824 
• Modeled Residue Count: 912 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoisopeptidase PeiR	A, B, C, D	228	Methanobrevibacter ruminantium M1	Mutation(s): 0  Gene Names: peiR, mru_0320
UniProt
Find proteins for D3DZZ6 (Methanobrevibacter ruminantium (strain ATCC 35063 / DSM 1093 / JCM 13430 / OCM 146 / M1)) Explore D3DZZ6  Go to UniProtKB:  D3DZZ6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.285 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.828	α = 90
b = 86.916	β = 91.85
c = 87.993	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-04-23 
Deposition Author(s): Guo, L.Z., Wang, S.X., Bai, L.p.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	42203080
National Natural Science Foundation of China (NSFC)	China	31970066

Revision History  

• Version 1.0: 2025-04-23
  Type: Initial release