8Z4N | pdb_00008z4n

Pseudomurein Endoisopeptidase PeiR-C90A

PDB DOI: https://doi.org/10.2210/pdb8Z4N/pdb

Classification: HYDROLASE
Organism(s): Methanobrevibacter ruminantium M1
Expression System: Escherichia coli
Mutation(s): Yes

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: 2.00 Å
R-Value Free:
0.235 (Depositor)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.200 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history.

Literature

Pseudomurein Endoisopeptidase PeiR-C90A

Guo, L.Z., Wang, S.X., Bai, L.p.

To be published.

Macromolecule Content

Total Structure Weight: 104.96 kDa
Atom Count: 8,058
Modeled Residue Count: 912
Deposited Residue Count: 912
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoisopeptidase PeiR	A, B, C, D	228	Methanobrevibacter ruminantium M1	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D3DZZ6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.235 (Depositor)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.479	α = 90
b = 88.025	β = 91.63
c = 87.412	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-23

Deposition Author(s):

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 (Full details and data files)

Version 1.0: 2025-04-23
Type: Initial release
Version 2.0: 2026-05-06
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary

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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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.