7X4R | pdb_00007x4r

Crystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase

PDB DOI: https://doi.org/10.2210/pdb7X4R/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-03-03 Released: 2023-09-13
Deposition Author(s): Liu, S., Wang, Y., Du, G., Wen, B., Xin, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.228 (Depositor), 0.235 (DCC)
R-Value Work:
0.191 (Depositor)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple motifs

Liu, S., Wen, B., Xin, F.

To be published.

Macromolecule Content

Total Structure Weight: 343.3 kDa
Atom Count: 22,150
Modeled Residue Count: 2,756
Deposited Residue Count: 3,012
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate decarboxylase	A, B, C, D, E A, B, C, D, E, F	502	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 Gene Names: BT_2570 EC: 4.1.1.15
UniProt
Find proteins for Q8A4M9 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A4M9 Go to UniProtKB: Q8A4M9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A4M9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.228 (Depositor), 0.235 (DCC)
R-Value Work: 0.191 (Depositor)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.064	α = 90
b = 132.189	β = 100.35
c = 109.892	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	S2020JBKY-13

Revision History (Full details and data files)

Version 1.0: 2023-09-13
Type: Initial release
Version 1.1: 2026-03-04
Changes: 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.