4JDU | pdb_00004jdu

The crystal structure of an aerotolerance-related membrane protein from Bacteroides fragilis NCTC 9343 with multiple mutations to serines.

PDB DOI: https://doi.org/10.2210/pdb4JDU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bacteroides fragilis NCTC 9343
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-02-25 Released: 2013-03-27
Deposition Author(s): Fan, Y., Tan, K., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.198 (Depositor), 0.214 (DCC)
R-Value Work:
0.182 (Depositor)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of an aerotolerance-related membrane protein from Bacteroides fragilis NCTC 9343 with multiple mutations to serines.

Fan, Y., Tan, K., Bigelow, L., Bearden, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 23.22 kDa
Atom Count: 1,661
Modeled Residue Count: 201
Deposited Residue Count: 215
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aerotolerance-related membrane protein	A	215	Bacteroides fragilis NCTC 9343	Mutation(s): 6 Gene Names: batB, BF2500, BF9343_2419
UniProt
Find proteins for Q5LCG5 (Bacteroides fragilis (strain ATCC 25285 / DSM 2151 / CCUG 4856 / JCM 11019 / LMG 10263 / NCTC 9343 / Onslow / VPI 2553 / EN-2)) Explore Q5LCG5 Go to UniProtKB: Q5LCG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5LCG5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.198 (Depositor), 0.214 (DCC)
R-Value Work: 0.182 (Depositor)
R-Value Observed: 0.182 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.277	α = 90
b = 49.871	β = 90
c = 85.451	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, 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.