PDB-7x51: Crystal structure of Bacteroides thetaiotaomicron glutamate decar...

ID or keywords:

Entry

Database: PDB / ID: 7x51

Title

Crystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase BTGAD-PLP-GUA complex

Components

Glutamate decarboxylase

Keywords

BIOSYNTHETIC PROTEIN / complex / glutarate / plp

Function / homology

Function and homology information

glutamate decarboxylase / glutamate decarboxylase activity / glutamate catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function

Biological species

Bacteroides thetaiotaomicron VPI-5482 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Liu, S. / Du, G. / Wang, L. / Wen, B. / Xin, F.

Funding support

China, 1items

Citation

Journal: Food Chem / Year: 2023
Title: Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple elements under different pH.
Authors: Liu, S. / Wen, B. / Du, G. / Wang, Y. / Ma, X. / Yu, H. / Zhang, J. / Fan, S. / Zhou, H. / Xin, F.

History

Deposition	Mar 3, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 19, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7x51.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7x51.ent.gz	956 KB	Display	PDB format
PDBx/mmJSON format	7x51.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7x51_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	7x51_full_validation.pdf.gz	4.1 MB	Display
Data in XML	7x51_validation.xml.gz	111.8 KB	Display
Data in CIF	7x51_validation.cif.gz	160.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x5/7x51 ftp://data.pdbj.org/pub/pdb/validation_reports/x5/7x51	HTTPS FTP

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Related structure data

Related structure data	7x4lC 7x4yC 7x52C 1pmmS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Glutamate decarboxylase

B: Glutamate decarboxylase

C: Glutamate decarboxylase

D: Glutamate decarboxylase

E: Glutamate decarboxylase

F: Glutamate decarboxylase

hetero molecules

332 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	109.820, 131.416, 109.839
Angle α, β, γ (deg.)	90.00, 100.19, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Glutamate decarboxylase Mass: 54913.844 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_2570 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A4M9, glutamate decarboxylase
#2: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₂O₄
#3: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GUA / GLUTARIC ACID Mass: 132.115 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₅H₈O₄ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1804 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.48 Å³/Da / Density % sol: 50.48 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.52 / Details: 13% PEG 3350, 0.1M pH4.52 sodium malonate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL18U1 / Wavelength: 0.979 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 206750 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.992 / CC star: 0.998 / R_merge(I) obs: 0.11 / R_pim(I) all: 0.045 / R_rim(I) all: 0.119 / Χ²: 0.576 / Net I/σ(I): 3.5 / Num. measured all: 1409197

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2-2.07	6.3	0.555	20616	0.827	0.952	0.238	0.605	0.433	100
2.07-2.15	6.9	0.443	20603	0.894	0.971	0.18	0.478	0.439	100
2.15-2.25	7	0.353	20591	0.926	0.981	0.142	0.381	0.467	100
2.25-2.37	6.9	0.276	20608	0.951	0.987	0.113	0.299	0.486	100
2.37-2.52	6.5	0.217	20653	0.965	0.991	0.092	0.236	0.518	99.9
2.52-2.71	7	0.179	20658	0.977	0.994	0.073	0.194	0.552	100
2.71-2.99	7	0.136	20630	0.986	0.996	0.055	0.147	0.607	100
2.99-3.42	6.7	0.098	20695	0.992	0.998	0.041	0.106	0.718	100
3.42-4.31	7.1	0.07	20740	0.996	0.999	0.028	0.076	0.819	100
4.31-50	6.7	0.055	20956	0.997	0.999	0.023	0.06	0.703	99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.19.1_4122: ???)	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
HKL-2000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PMM

1pmm

Resolution: 2→36.04 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 23.45 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2389	10066	4.87 %
R_work	0.2012	-	-
obs	0.203	206662	99.87 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→36.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22156	0	35	1804	23995

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	22774
X-RAY DIFFRACTION	f_angle_d	0.925	30976
X-RAY DIFFRACTION	f_dihedral_angle_d	13.325	8299
X-RAY DIFFRACTION	f_chiral_restr	0.054	3321
X-RAY DIFFRACTION	f_plane_restr	0.008	3962

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.02	0.302	328	0.2415	6348	X-RAY DIFFRACTION	97
2.02-2.05	0.3025	332	0.2467	6519	X-RAY DIFFRACTION	100
2.05-2.07	0.2647	360	0.2242	6545	X-RAY DIFFRACTION	100
2.07-2.1	0.27	320	0.2238	6505	X-RAY DIFFRACTION	100
2.1-2.12	0.2741	361	0.2249	6500	X-RAY DIFFRACTION	100
2.12-2.15	0.2715	373	0.2264	6560	X-RAY DIFFRACTION	100
2.15-2.18	0.2493	316	0.2189	6535	X-RAY DIFFRACTION	100
2.18-2.22	0.2474	380	0.2099	6462	X-RAY DIFFRACTION	100
2.22-2.25	0.2549	360	0.2098	6560	X-RAY DIFFRACTION	100
2.25-2.29	0.2533	297	0.1993	6626	X-RAY DIFFRACTION	100
2.29-2.33	0.2374	330	0.2001	6515	X-RAY DIFFRACTION	100
2.33-2.37	0.2671	337	0.2046	6521	X-RAY DIFFRACTION	100
2.37-2.42	0.2512	305	0.2088	6584	X-RAY DIFFRACTION	100
2.42-2.46	0.2576	344	0.2097	6532	X-RAY DIFFRACTION	100
2.46-2.52	0.2672	321	0.2122	6571	X-RAY DIFFRACTION	100
2.52-2.58	0.2362	324	0.2029	6539	X-RAY DIFFRACTION	100
2.58-2.64	0.2359	324	0.1948	6563	X-RAY DIFFRACTION	100
2.64-2.71	0.256	365	0.199	6556	X-RAY DIFFRACTION	100
2.71-2.79	0.2521	307	0.1991	6572	X-RAY DIFFRACTION	100
2.79-2.88	0.2461	373	0.2102	6536	X-RAY DIFFRACTION	100
2.88-2.99	0.2554	319	0.2054	6550	X-RAY DIFFRACTION	100
2.99-3.1	0.2486	312	0.2114	6579	X-RAY DIFFRACTION	100
3.1-3.25	0.2251	357	0.2004	6570	X-RAY DIFFRACTION	100
3.25-3.42	0.2381	291	0.1988	6605	X-RAY DIFFRACTION	100
3.42-3.63	0.2247	334	0.1914	6564	X-RAY DIFFRACTION	100
3.63-3.91	0.2127	351	0.1842	6589	X-RAY DIFFRACTION	100
3.91-4.3	0.2072	338	0.18	6567	X-RAY DIFFRACTION	100
4.3-4.93	0.2036	310	0.1859	6625	X-RAY DIFFRACTION	100
4.93-6.2	0.2185	323	0.2004	6658	X-RAY DIFFRACTION	100
6.2-36.04	0.2563	374	0.2052	6640	X-RAY DIFFRACTION	100

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