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- PDB-1pmm: Crystal structure of Escherichia coli GadB (low pH) -

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Basic information

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


glutamate decarboxylase / glutamate decarboxylase activity / intracellular pH elevation / L-glutamate catabolic process / 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
ACETIC ACID / PYRIDOXAL-5'-PHOSPHATE / Glutamate decarboxylase beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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: Non-polymer description / Version format compliance
Revision 1.3Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)318,21118
Polymers316,3686
Non-polymers1,84312
Water33,1841842
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48750 Å2
ΔGint-209 kcal/mol
Surface area86180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.780, 91.406, 93.686
Angle α, β, γ (deg.)76.80, 77.10, 78.24
Int Tables number1
Space group name H-MP1
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
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1842 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium formate, sodium acetate, PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
2100 mMsodium acetate1droppH4.6
3135 mMsodium acetate1reservoirpH4.6
4700 mMsodium formate1reservoir
513 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003 / Details: DYNAMICALLY BENDABLE MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→24.62 Å / Num. obs: 178481 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 6.3 / Num. unique all: 17609 / % possible all: 94.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å
Reflection shell
*PLUS
Highest resolution: 2 Å / Mean I/σ(I) obs: 6.2

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Processing

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

Resolution: 2→24.62 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5238 -RANDOM
Rwork0.182 ---
obs-178480 95.8 %-
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.377 Å20.506 Å2-0.253 Å2
2---0.376 Å2-0.349 Å2
3----0.124 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→24.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21444 0 114 1842 23400
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.23
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection
Rfree0.187 148
Rwork0.225 -
obs-5023
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 25 Å / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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