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- PDB-7x4r: Crystal structure of Bacteroides thetaiotaomicron glutamate decar... -

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Basic information

Entry
Database: PDB / ID: 7x4r
TitleCrystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase
ComponentsGlutamate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / glutamate decarboxylase
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / L-glutamate catabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Glutamate decarboxylase / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamate decarboxylase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLiu, S. / Wang, Y. / Du, G. / Wen, B. / Xin, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentS2020JBKY-13 China
CitationJournal: To Be Published
Title: Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple motifs
Authors: Liu, S. / Wen, B. / Xin, F.
History
DepositionMar 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate decarboxylase
B: Glutamate decarboxylase
C: Glutamate decarboxylase
D: Glutamate decarboxylase
E: Glutamate decarboxylase
F: Glutamate decarboxylase


Theoretical massNumber of molelcules
Total (without water)343,2986
Polymers343,2986
Non-polymers00
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area49030 Å2
ΔGint-277 kcal/mol
Surface area82290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.064, 132.189, 109.892
Angle α, β, γ (deg.)90.000, 100.350, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glutamate decarboxylase


Mass: 57216.395 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 15% PEG 3350, 6% pH4.0 TacsimateTM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.14
ReflectionResolution: 2.6→50 Å / Num. obs: 92291 / % possible obs: 95.8 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.064 / Rrim(I) all: 0.133 / Χ2: 0.962 / Net I/σ(I): 9.6 / Num. measured all: 376488
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.693.90.76393590.7670.4280.880.71597
2.69-2.840.55192610.8450.3030.6320.7697.3
2.8-2.934.20.44693330.9080.240.5090.79696.9
2.93-3.084.20.35591610.9240.1910.4050.89195.4
3.08-3.2840.2590440.9590.140.2880.98494.6
3.28-3.534.10.17890490.9760.0990.2051.11193.9
3.53-3.884.10.12589000.9860.070.1451.17692.9
3.88-4.453.90.08590950.9910.050.0991.15294.1
4.45-5.64.30.06794550.9930.0370.0771.0597.9
5.6-504.20.05996340.9940.0340.0680.9998.4

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PMM

1pmm


Resolution: 2.6→48.65 Å / Cross valid method: THROUGHOUT / σ(F): 57.92 / Phase error: 30.3 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2277 4870 5.28 %
Rwork0.1908 87546 -
obs0.1956 92265 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.28 Å2 / Biso mean: 57.9779 Å2 / Biso min: 19.35 Å2
Refinement stepCycle: final / Resolution: 2.6→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21848 0 0 302 22150
Biso mean---48.95 -
Num. residues----2750
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.630.33072460.2996398682
2.63-2.680.32522260.2891447392
2.68-2.730.29272070.2734443493
2.73-2.780.30182400.2667443392
2.78-2.850.31092280.2616442792
2.85-2.910.31212150.2638449592
2.91-2.980.32022290.259439891
2.98-3.060.2982270.2556440190
3.06-3.150.28272340.2432427590
3.15-3.260.26262120.2402435090
3.26-3.370.26052390.2141432989
3.37-3.510.24472270.2045429389
3.51-3.670.232300.1836425588
3.67-3.860.24152230.181423189
3.86-4.10.19262480.1628427088
4.1-4.420.18572630.1434436390
4.42-4.860.19422450.1459444792
4.86-5.570.20172420.1634454994
5.57-7.010.24092730.1868457694
7.01-48.650.17582650.1624456192

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