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- PDB-7x4l: Crystal structure of Bacteroides thetaiotaomicron glutamate decar... -

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Basic information

Entry
Database: PDB / ID: 7x4l
TitleCrystal structure of Bacteroides thetaiotaomicron glutamate decarboxylase mutant Y303F-PLP complex
ComponentsGlutamate decarboxylase
KeywordsBIOSYNTHETIC PROTEIN / PLP / Complex / Neutral
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
PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLiu, S. / Guoming, D. / Yulu, W. / Boting, W. / Xin, F.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentS2020JBKY-13 China
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.
#1: Journal: Food Chem / Year: 2023
Title: Coordinated regulation of Bacteroides thetaiotaomicron glutamate decarboxylase activity by multiple elements under different pH
Authors: Liu, S. / Guoming, D. / Yulu, W. / Boting, W. / Xin, F.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 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)330,87012
Polymers329,3876
Non-polymers1,4836
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38700 Å2
ΔGint-245 kcal/mol
Surface area90410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.449, 176.383, 176.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Glutamate decarboxylase /


Mass: 54897.844 Da / Num. of mol.: 6 / Mutation: Y303F
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.68 Å3/Da / Density % sol: 66.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% PEG MME 2000, 0.1M pH7.0 Imidole, 0.2M Ammonium citrate, 1% Ethyl acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 150645 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.086 / Χ2: 0.775 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.6960.732149020.7870.9380.3220.8010.44699.8
2.69-2.86.20.525148970.8880.970.2240.5720.47199.8
2.8-2.936.30.369149090.9360.9830.1570.4020.53599.8
2.93-3.086.10.266149630.9640.9910.1150.290.64299.8
3.08-3.286.20.175150090.9820.9950.0760.1910.77699.8
3.28-3.536.50.12150240.9910.9980.0510.130.91999.9
3.53-3.886.20.082150510.9950.9990.0360.090.91599.9
3.88-4.456.50.06151200.9970.9990.0260.0651.103100
4.45-5.66.30.05152070.9980.9990.0210.0550.93699.9
5.6-505.60.041155630.99810.0190.0460.96699.2

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PMM

1pmm


Resolution: 2.59→29.4 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 7436 4.94 %
Rwork0.2034 --
obs0.2039 150435 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→29.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21281 0 0 249 21530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321866
X-RAY DIFFRACTIONf_angle_d0.62929801
X-RAY DIFFRACTIONf_dihedral_angle_d12.9397829
X-RAY DIFFRACTIONf_chiral_restr0.0453239
X-RAY DIFFRACTIONf_plane_restr0.0053781
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.620.30252080.3034083X-RAY DIFFRACTION87
2.62-2.650.29392440.28834768X-RAY DIFFRACTION100
2.65-2.680.2742250.29144756X-RAY DIFFRACTION100
2.68-2.710.28542430.28094752X-RAY DIFFRACTION100
2.71-2.750.3022460.27124733X-RAY DIFFRACTION100
2.75-2.790.26422330.26844743X-RAY DIFFRACTION100
2.79-2.830.27623120.26524702X-RAY DIFFRACTION100
2.83-2.870.26132660.27244749X-RAY DIFFRACTION100
2.87-2.910.27332530.27484714X-RAY DIFFRACTION100
2.91-2.960.28532840.27364692X-RAY DIFFRACTION100
2.96-3.010.28622640.2654772X-RAY DIFFRACTION100
3.01-3.070.29032500.26494745X-RAY DIFFRACTION100
3.07-3.130.262250.25674760X-RAY DIFFRACTION100
3.13-3.190.2642800.26044756X-RAY DIFFRACTION100
3.19-3.260.2662550.25324745X-RAY DIFFRACTION100
3.26-3.330.27362480.24954780X-RAY DIFFRACTION100
3.33-3.420.26782120.23724835X-RAY DIFFRACTION100
3.42-3.510.24592600.2244779X-RAY DIFFRACTION100
3.51-3.610.212200.22084819X-RAY DIFFRACTION100
3.61-3.730.2272690.21464750X-RAY DIFFRACTION100
3.73-3.860.20142410.19844789X-RAY DIFFRACTION100
3.86-4.020.20582040.19064850X-RAY DIFFRACTION100
4.02-4.20.19862490.17154839X-RAY DIFFRACTION100
4.2-4.420.17541990.17394830X-RAY DIFFRACTION100
4.42-4.70.17372710.17294810X-RAY DIFFRACTION100
4.7-5.060.1822220.16854844X-RAY DIFFRACTION100
5.06-5.560.18812610.17354859X-RAY DIFFRACTION100
5.56-6.360.19112520.17524881X-RAY DIFFRACTION100
6.36-7.990.17822690.17194907X-RAY DIFFRACTION100
7.99-29.40.15782710.15324957X-RAY DIFFRACTION97

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