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- PDB-5gp4: Lactobacillus brevis CGMCC 1306 Glutamate decarboxylase -

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Basic information

Entry
Database: PDB / ID: 5gp4
TitleLactobacillus brevis CGMCC 1306 Glutamate decarboxylase
ComponentsGlutamate decarboxylase
KeywordsLYASE / Glutamate decarboxylase Lactobacillus brevis CGMCC 1306 Gamma-aminobutyric acid pyridoxal phosphate (PLP)
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / glutamate metabolic process / pyridoxal phosphate binding
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
PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsMei, L. / Huang, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21176220 and 31470793 China
the Natural Science Foundation of Zhejiang ProvinceZ13B060008 and LY16B060008 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2018
Title: Lactobacillus brevis CGMCC 1306 glutamate decarboxylase: Crystal structure and functional analysis.
Authors: Huang, J. / Fang, H. / Gai, Z.C. / Mei, J.Q. / Li, J.N. / Hu, S. / Lv, C.J. / Zhao, W.R. / Mei, L.H.
History
DepositionJul 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Glutamate decarboxylase
A: Glutamate decarboxylase
B: Glutamate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5796
Polymers160,8383
Non-polymers7413
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14520 Å2
ΔGint-51 kcal/mol
Surface area50440 Å2
2
C: Glutamate decarboxylase
A: Glutamate decarboxylase
B: Glutamate decarboxylase
hetero molecules

C: Glutamate decarboxylase
A: Glutamate decarboxylase
B: Glutamate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,15912
Polymers321,6766
Non-polymers1,4836
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area45160 Å2
ΔGint-159 kcal/mol
Surface area84740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.333, 170.129, 164.567
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutamate decarboxylase


Mass: 53612.664 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: gad / Plasmid: pet28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: D6PXK5, glutamate decarboxylase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10% W/V PEG 2000 MME, 100mM Sodium Acetate/Acetic acid, 200mM Ammonium Sulfate

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Data collection

DiffractionMean temperature: 82 K / Ambient temp details: 82
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97851 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97851 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 85974 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.93 / Rmerge(I) obs: 0.176 / Net I/σ(I): 10.88
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.7 / CC1/2: 0.84 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data collection
SCALEPACKdata scaling
PHASERphasing
MERLOTdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xey

1xey


Resolution: 2.16→48.543 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 5.117 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23005 4290 5 %RANDOM
Rwork0.18694 ---
obs0.18911 81517 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å2-0 Å2
2---0.35 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.16→48.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10498 0 45 185 10728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910809
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210051
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.95114687
X-RAY DIFFRACTIONr_angle_other_deg1.188323095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61851301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44923.992531
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.737151792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7051565
X-RAY DIFFRACTIONr_chiral_restr0.1420.21583
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022560
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8692.9185213
X-RAY DIFFRACTIONr_mcbond_other2.8672.9185212
X-RAY DIFFRACTIONr_mcangle_it4.2534.3576511
X-RAY DIFFRACTIONr_mcangle_other4.2544.3586512
X-RAY DIFFRACTIONr_scbond_it3.5933.3155594
X-RAY DIFFRACTIONr_scbond_other3.5923.3155595
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.564.8118177
X-RAY DIFFRACTIONr_long_range_B_refined6.98822.76512283
X-RAY DIFFRACTIONr_long_range_B_other6.98822.76512284
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.156→2.212 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 290 -
Rwork0.239 5558 -
obs--92.87 %

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