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- PDB-7x52: Crystal structure of Bacteroides thetaiotaomicron glutamate decar... -

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Basic information

Entry
Database: PDB / ID: 7x52
TitleCrystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase BTGAD-PLP complex
ComponentsGlutamate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / complex / plp
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / 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
ACETATE ION / MALONATE ION / 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)345,50122
Polymers343,2986
Non-polymers2,20216
Water31,9591774
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area53840 Å2
ΔGint-274 kcal/mol
Surface area81360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.765, 131.267, 109.853
Angle α, β, γ (deg.)90.000, 100.280, 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: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1774 / 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 19% PEG 3350, 1% pH4.0 TacsimateTM, 0.1M pH4.35 Sodium acetate

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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: 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: 238249 / % possible obs: 98.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.041 / Rrim(I) all: 0.082 / Χ2: 0.902 / Net I/σ(I): 7 / Num. measured all: 906940
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.70.526237550.80.3060.6110.70998.9
1.97-2.053.70.364236970.880.2150.4240.73898.7
2.05-2.143.80.275237910.9290.160.320.80198.9
2.14-2.253.90.205238290.9590.1160.2360.80599.2
2.25-2.393.80.148238590.9770.0860.1720.8599.1
2.39-2.583.70.112236540.9840.0660.130.92198.5
2.58-2.8440.086238760.9910.0490.0990.9799.2
2.84-3.253.80.065238840.9940.0380.0751.03198.9
3.25-4.0940.05239760.9960.0280.0581.09299.2
4.09-503.80.044239280.9960.0260.0511.07698.1

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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: 1.9→36 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1943 12067 5.07 %
Rwork0.1649 226055 -
obs0.1664 238122 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.54 Å2 / Biso mean: 34.2526 Å2 / Biso min: 14.68 Å2
Refinement stepCycle: final / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22021 0 139 1774 23934
Biso mean--32.49 38.62 -
Num. residues----2744
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 (%)
1.9-1.920.28193730.22867172754595
1.92-1.940.2673800.22327542792299
1.94-1.970.2483980.21887564796299
1.97-1.990.24413820.2057506788899
1.99-2.020.23533790.20117533791299
2.02-2.040.24394460.20427441788799
2.04-2.070.23173720.18697525789798
2.07-2.10.20874330.17967503793699
2.1-2.140.20674160.17747563797999
2.14-2.170.2254120.17817539795199
2.17-2.210.21673240.16977654797899
2.21-2.250.20353600.16417599795999
2.25-2.290.20634280.16797534796299
2.29-2.340.2093780.17037561793999
2.34-2.390.24373990.17127615801499
2.39-2.450.21013930.16867553794699
2.45-2.510.1994100.16847385779597
2.51-2.570.19974410.16967490793199
2.57-2.650.21264110.16797538794999
2.65-2.740.19234530.16357550800399
2.74-2.830.21383870.16997573796099
2.83-2.950.21594190.16767613803299
2.95-3.080.21534110.173275507961100
3.08-3.240.20223840.16777543792798
3.24-3.450.17454160.15867544796099
3.45-3.710.18494060.14717587799399
3.71-4.090.15164330.14297605803899
4.09-4.680.16053930.14157552794599
4.68-5.890.17924440.15667534797898
5.89-360.17483860.16717587797397

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