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- PDB-1pmo: Crystal structure of Escherichia coli GadB (neutral pH) -

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Basic information

Entry
Database: PDB / ID: 1pmo
TitleCrystal structure of Escherichia coli GadB (neutral pH)
ComponentsGlutamate decarboxylase beta
KeywordsLYASE / NEUTRAL-PH FORM OF GadB
Function / homology
Function and homology information


glutamate decarboxylase / glutamate decarboxylase activity / glutamate catabolic process / intracellular pH elevation / pyridoxal phosphate binding / membrane / cytosol
Similarity search - Function
MYOD Basic-Helix-Loop-Helix Domain, subunit B - #50 / Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 ...MYOD Basic-Helix-Loop-Helix Domain, subunit B - #50 / Aspartate Aminotransferase, domain 1 - #160 / Glutamate decarboxylase / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / MYOD Basic-Helix-Loop-Helix Domain, subunit B / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Few Secondary Structures / Irregular / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PLR / Glutamate decarboxylase beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsCapitani, G. / De Biase, D. / Aurizi, C. / Gut, H. / Bossa, F. / Grutter, M.G.
CitationJournal: Embo J. / Year: 2003
Title: Crystal structure and functional analysis of escherichia coli glutamate decarboxylase
Authors: Capitani, G. / De Biase, D. / Aurizi, C. / Gut, H. / Bossa, F. / Grutter, M.G.
History
DepositionJun 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate decarboxylase beta
B: Glutamate decarboxylase beta
C: Glutamate decarboxylase beta
D: Glutamate decarboxylase beta
E: Glutamate decarboxylase beta
F: Glutamate decarboxylase beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,96530
Polymers316,3686
Non-polymers3,59824
Water21,0601169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area56230 Å2
ΔGint-138 kcal/mol
Surface area84340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.995, 115.995, 207.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsTHE BIOLOGICAL ASSEMBLY IS A HEXAMER

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Components

#1: Protein
Glutamate decarboxylase beta / GAD-beta


Mass: 52727.957 Da / Num. of mol.: 6 / Fragment: GadB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: GADB / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69910, glutamate decarboxylase
#2: Chemical
ChemComp-PLR / (5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE / 4'-DEOXYPYRIDOXINE PHOSPHATE


Mass: 233.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H12NO5P
#3: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1169 / 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: 2.54 Å3/Da / Density % sol: 51.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: ammonium sulphate, Tris, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
21.9-2.0 Mammonium sulfate1reservoir
3100 mMTris1reservoirpH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 1999 / Details: MULTILAYER
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 136345 / Num. obs: 136310 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 8.1
Reflection shellResolution: 2.3→2.35 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.1 / Num. unique all: 9117 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 136345
Reflection shell
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD
Starting model: NULL

Resolution: 2.3→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2749 -RANDOM
Rwork0.2 ---
obs-136306 98.9 %-
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.593 Å2-3.585 Å20 Å2
2---0.593 Å20 Å2
3---1.186 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21799 0 234 1169 23202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection
Rfree0.301 269
Rwork0.263 -
obs-13072
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0065
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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