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- PDB-8zuw: Crystal structure of Bacteroides thetaiotaomicron glutamate decar... -

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Basic information

Entry
Database: PDB / ID: 8zuw
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 / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Glutamate decarboxylase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsLiu, S. / Yulu, W. / Guoming, D. / Boting, W. / Xin, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple motifs
Authors: Liu, S. / Boting, W. / Xin, F.
History
DepositionJun 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 11, 2025Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,25214
Polymers329,4836
Non-polymers7698
Water12,917717
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48730 Å2
ΔGint-431 kcal/mol
Surface area82070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.228, 124.897, 109.622
Angle α, β, γ (deg.)90.00, 100.52, 90.00
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 (bacteria)
Gene: DW780_22950, GAN91_24535, GAO51_14925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0P0FKB9, glutamate decarboxylase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 717 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 16% (w/v) PEG3350/0.06M Citric acid/0.04 M BIS-Tris propane pH 4.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021
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: 0.12
ReflectionResolution: 2.44→50.15 Å / Num. obs: 100824 / % possible obs: 96.4 % / Redundancy: 4.2 % / CC1/2: 0.952 / CC star: 0.988 / Rmerge(I) obs: 0.196 / Rpim(I) all: 0.102 / Rrim(I) all: 0.222 / Χ2: 0.925 / Net I/σ(I): 3.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.44-2.482.50.33442950.7190.9150.2280.4070.5982.2
2.48-2.5330.36749280.7110.9120.2330.4380.56293.9
2.53-2.583.60.37950590.730.9190.2240.4430.55697.7
2.58-2.633.90.37650720.7610.930.2110.4340.58398
2.63-2.694.20.37650940.7960.9410.2030.4290.58498
2.69-2.754.40.3551040.8410.9560.1840.3970.63598.3
2.75-2.824.40.34351220.850.9590.1790.3890.63998
2.82-2.894.40.32251100.870.9650.1680.3650.6997.9
2.89-2.984.40.31251200.8760.9660.1630.3540.72298.4
2.98-3.074.40.28251010.8920.9710.1480.320.80897.8
3.07-3.184.10.26149840.9060.9750.1410.2980.97195.4
3.18-3.314.30.23549350.9260.9810.1240.2671.06494.7
3.31-3.464.70.21651550.9480.9870.110.2431.13898.4
3.46-3.644.70.19951870.9540.9880.1010.2241.19298.6
3.64-3.874.60.18451430.9570.9890.0940.2071.23398.5
3.87-4.174.60.16951240.9630.9910.0870.1911.20198.1
4.17-4.594.30.15150590.9650.9910.0810.1721.22796.9
4.59-5.254.40.14949510.9680.9920.0780.1691.22494.4
5.25-6.624.80.15752060.9630.9910.0790.1761.14598.3
6.62-504.50.13650750.9760.9940.0690.1531.12394.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7X52

7x52


Resolution: 2.46→50.15 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 429.22 / Phase error: 27.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2336 5272 5.23 %
Rwork0.1811 --
obs0.1864 100781 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→50.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21828 0 40 717 22585
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922454
X-RAY DIFFRACTIONf_angle_d1.05730590
X-RAY DIFFRACTIONf_dihedral_angle_d13.0928086
X-RAY DIFFRACTIONf_chiral_restr0.0593323
X-RAY DIFFRACTIONf_plane_restr0.0083903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.50.31512070.24693714X-RAY DIFFRACTION71
2.5-2.550.27172410.24434617X-RAY DIFFRACTION88
2.55-2.60.26872480.24064861X-RAY DIFFRACTION93
2.6-2.650.2792910.23024790X-RAY DIFFRACTION92
2.65-2.710.28482510.22194848X-RAY DIFFRACTION93
2.71-2.770.24412770.21974883X-RAY DIFFRACTION93
2.77-2.840.25722850.21544852X-RAY DIFFRACTION93
2.84-2.920.28112210.21144893X-RAY DIFFRACTION94
2.92-30.24932540.21194898X-RAY DIFFRACTION94
3-3.10.23822530.20664865X-RAY DIFFRACTION93
3.1-3.210.26632790.19974780X-RAY DIFFRACTION91
3.21-3.340.25582560.19574683X-RAY DIFFRACTION89
3.34-3.490.2282230.18564929X-RAY DIFFRACTION94
3.49-3.670.22132870.1744902X-RAY DIFFRACTION93
3.67-3.90.19432200.16064953X-RAY DIFFRACTION94
3.9-4.20.20612300.14694935X-RAY DIFFRACTION94
4.2-4.630.19972520.1434841X-RAY DIFFRACTION92
4.63-5.30.19022610.14744711X-RAY DIFFRACTION89
5.3-6.670.24663060.17834915X-RAY DIFFRACTION93
6.67-50.150.23152480.17574821X-RAY DIFFRACTION90

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