9IY9 | pdb_00009iy9

Crystal structure of a putative endopeptidase from Bacteroides fragilis

PDB DOI: https://doi.org/10.2210/pdb9IY9/pdb

Classification: HYDROLASE
Organism(s): Bacteroides fragilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-30 Released: 2025-08-06
Deposition Author(s): Oh, H., Hong, M.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.248 (Depositor), 0.252 (DCC)
R-Value Work:
0.192 (Depositor), 0.195 (DCC)
R-Value Observed:
0.194 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of a putative endopeptidase from Bacteroides fragilis

Oh, H., Hong, M.

To be published.

Macromolecule Content

Total Structure Weight: 47.44 kDa
Atom Count: 3,311
Modeled Residue Count: 420
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exported protein	A	420	Bacteroides fragilis	Mutation(s): 0 Gene Names: BF9343_2581
UniProt
Find proteins for Q5LC06 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LC06 Go to UniProtKB: Q5LC06
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5LC06
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 2.60 Å
R-Value Free: 0.248 (Depositor), 0.252 (DCC)
R-Value Work: 0.192 (Depositor), 0.195 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.867	α = 90
b = 102.867	β = 90
c = 161.968	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-08-06

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1F1A1045940

Revision History (Full details and data files)

Version 1.0: 2025-08-06
Type: Initial release

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.