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- PDB-1szk: The structure of gamma-aminobutyrate aminotransferase mutant: E211S -

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Basic information

Entry
Database: PDB / ID: 1szk
TitleThe structure of gamma-aminobutyrate aminotransferase mutant: E211S
Components4-aminobutyrate aminotransferase
KeywordsTRANSFERASE / GABA-AT
Function / homology
Function and homology information


5-aminovalerate transaminase / 5-aminovalerate transaminase activity / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity / gamma-aminobutyric acid catabolic process / L-arginine biosynthetic process via ornithine / pyridoxal phosphate binding / protein homodimerization activity / cytosol
Similarity search - Function
4-aminobutyrate aminotransferase, bacterial / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...4-aminobutyrate aminotransferase, bacterial / : / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate aminotransferase GabT
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsLiu, W. / Peterson, P.E. / Langston, J.A. / Jin, X. / Fisher, A.J. / Toney, M.D.
CitationJournal: Biochemistry / Year: 2005
Title: Kinetic and Crystallographic Analysis of Active Site Mutants of Escherichia coligamma-Aminobutyrate Aminotransferase.
Authors: Liu, W. / Peterson, P.E. / Langston, J.A. / Jin, X. / Zhou, X. / Fisher, A.J. / Toney, M.D.
History
DepositionApr 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 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

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Assembly

Deposited unit
A: 4-aminobutyrate aminotransferase
B: 4-aminobutyrate aminotransferase
C: 4-aminobutyrate aminotransferase
D: 4-aminobutyrate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,38236
Polymers183,1424
Non-polymers3,24132
Water12,124673
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31320 Å2
ΔGint-265 kcal/mol
Surface area49040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.260, 108.260, 300.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
4-aminobutyrate aminotransferase / Gamma-amino-N-butyrate transaminase / GABA transaminase / Glutamate:succinic semialdehyde ...Gamma-amino-N-butyrate transaminase / GABA transaminase / Glutamate:succinic semialdehyde transaminase / GABA aminotransferase / GABA-AT


Mass: 45785.461 Da / Num. of mol.: 4 / Mutation: E211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET23a(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P22256, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / 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: 2.78 Å3/Da / Density % sol: 55.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: HEPES, Ammonium Sulfate, PLP, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2000
RadiationMonochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.52→30 Å / Num. all: 71654 / Num. obs: 69873 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Rsym value: 0.084 / Net I/σ(I): 12.4
Reflection shellResolution: 2.52→2.59 Å / % possible all: 97.5

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1SF2

1sf2


Resolution: 2.52→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 3515 Random
Rwork0.187 --
all0.188 71654 -
obs0.188 69873 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.374 Å2-5.059 Å20 Å2
2---4.374 Å20 Å2
3---8.748 Å2
Refinement stepCycle: LAST / Resolution: 2.52→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12824 0 191 673 13688
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_mcbond_it1.2151.5
X-RAY DIFFRACTIONc_mcangle_it2.0272
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it2.6412.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3pmp_so4_egl.par

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