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- PDB-7x4y: Crystal structure of Bacteroides thetaiotaomicron glutamate decar... -

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Basic information

Entry
Database: PDB / ID: 7x4y
TitleCrystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase BTGAD-PLP-GABA complex
ComponentsGlutamate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / complex / GABA
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
GAMMA-AMINO-BUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, S. / Du, G. / Wang, Y. / Wen, B. / Xin, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentS2020JBKY-13 China
CitationJournal: 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
DepositionMar 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,58518
Polymers329,4836
Non-polymers2,10212
Water27,2211511
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51490 Å2
ΔGint-266 kcal/mol
Surface area81990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.736, 130.689, 109.761
Angle α, β, γ (deg.)90.000, 100.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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-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
#3: Chemical
ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1511 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 13% PEG 3350, 7% pH4.0 TacsimateTM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 236110 / % possible obs: 99 % / Redundancy: 3.9 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.047 / Rrim(I) all: 0.093 / Χ2: 0.651 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.91-1.943.60.463117670.850.2830.5450.27999
1.94-1.983.70.43117750.8790.2590.5040.28999.4
1.98-2.023.70.359118570.9130.2150.420.31299.4
2.02-2.063.60.32118140.9060.1980.3770.33399.2
2.06-2.13.60.283117070.9290.1720.3320.36599
2.1-2.154.10.25118660.9570.1430.2890.38999.5
2.15-2.240.226118510.9580.1290.2610.41899.6
2.2-2.2640.197118320.9670.1130.2280.4799.3
2.26-2.3340.172118390.9690.10.20.50999.4
2.33-2.413.90.149118100.9770.0880.1740.54699.2
2.41-2.493.70.136117670.9760.0830.160.62698.7
2.49-2.593.80.121117060.9810.0720.1410.64698.5
2.59-2.714.10.113118400.9830.0650.1310.71399.3
2.71-2.8540.096118550.9870.0560.1120.76499.1
2.85-3.0340.088118110.9880.0520.1030.85899.1
3.03-3.273.70.077116870.9890.0470.0910.98797.8
3.27-3.5940.071118380.9910.0420.0831.10799.1
3.59-4.1140.062118970.9920.0370.0721.15599.3
4.11-5.183.80.056117430.9940.0340.0661.17297.7
5.18-5040.049118480.9960.0280.0570.94697.5

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Processing

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

1pmm


Resolution: 1.9→26.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 11697 4.96 %
Rwork0.1809 224331 -
obs0.1825 236028 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.72 Å2 / Biso mean: 37.5126 Å2 / Biso min: 18.19 Å2
Refinement stepCycle: final / Resolution: 1.9→26.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21987 0 132 1511 23630
Biso mean--33.66 40.14 -
Num. residues----2743
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.920.30723020.26165831613376
1.92-1.940.28863960.25937452784899
1.94-1.960.28294240.25417550797499
1.96-1.990.28744340.2387462789699
1.99-2.020.2923660.2317540790699
2.02-2.040.25993920.22777544793699
2.04-2.070.26944020.22087509791199
2.07-2.10.24714260.209175187944100
2.1-2.140.22623960.200275517947100
2.14-2.170.25043440.202975567900100
2.17-2.210.20333660.190876277993100
2.21-2.250.22574100.19077534794499
2.25-2.290.24854190.19597511793099
2.29-2.340.22354030.19247622802599
2.34-2.390.23464090.19117455786499
2.39-2.450.22924290.19557451788099
2.45-2.510.2183970.1957494789198
2.51-2.570.25893170.19217530784799
2.57-2.650.21824170.18717533795099
2.65-2.740.22513820.18387588797099
2.74-2.830.21464100.18917538794899
2.83-2.950.21994040.19057550795499
2.95-3.080.21823940.19027544793899
3.08-3.240.2244000.19377388778897
3.24-3.440.2053560.18087602795899
3.44-3.710.19673510.16747609796099
3.71-4.080.17673850.15467606799199
4.08-4.670.18843560.14977561791798
4.67-5.870.17824260.15697495792198
5.87-26.490.17613840.16147580796497

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