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- PDB-6j2v: GABA aminotransferase from Corynebacterium glutamicum -

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Basic information

Entry
Database: PDB / ID: 6j2v
TitleGABA aminotransferase from Corynebacterium glutamicum
ComponentsPLP-dependent aminotransferases
KeywordsTRANSFERASE
Function / homology
Function and homology information


4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
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) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, 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
Chem-PLZ / PLP-dependent aminotransferases
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHong, J. / Kim, K.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of gamma-aminobutyrate aminotransferase in complex with a PLP-GABA adduct from Corynebacterium glutamicum.
Authors: Hong, J. / Kim, K.J.
History
DepositionJan 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
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 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLP-dependent aminotransferases
B: PLP-dependent aminotransferases
C: PLP-dependent aminotransferases
D: PLP-dependent aminotransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,95416
Polymers198,8804
Non-polymers2,07412
Water24,6451368
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26170 Å2
ΔGint-114 kcal/mol
Surface area50070 Å2
2
A: PLP-dependent aminotransferases
B: PLP-dependent aminotransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4778
Polymers99,4402
Non-polymers1,0376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-60 kcal/mol
Surface area26510 Å2
MethodPISA
3
C: PLP-dependent aminotransferases
D: PLP-dependent aminotransferases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4778
Polymers99,4402
Non-polymers1,0376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11630 Å2
ΔGint-61 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.725, 70.495, 97.017
Angle α, β, γ (deg.)106.570, 96.480, 110.660
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PLP-dependent aminotransferases


Mass: 49720.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Strain: ATCC 13032 / Gene: Cgl0479 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NT35, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLZ / 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID


Mass: 334.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H19N2O7P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1368 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350, 0.1M BIS-Tris (pH6.5), 0.2M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 119202 / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.051 / Rrim(I) all: 0.097 / Χ2: 3.541 / Net I/σ(I): 14.6 / Num. measured all: 409512
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.10.29558010.870.1940.3541.65695.4
1.93-1.973.10.26358560.9010.1720.3151.77195.4
1.97-2.013.20.23259350.930.1490.2771.90696
2.01-2.053.30.20758700.9430.1320.2462.04496.3
2.05-2.093.30.19458750.9510.1230.232.14696.6
2.09-2.143.40.16860060.960.1050.1992.29596.7
2.14-2.193.40.14759720.9720.0910.1732.39396.9
2.19-2.253.40.13859260.9720.0860.1632.58696.8
2.25-2.323.40.1359230.9770.080.1532.71797.2
2.32-2.393.40.1259530.980.0740.1412.7697
2.39-2.483.40.11159750.9820.0690.1313.07197.3
2.48-2.583.40.10559640.9840.0650.1243.15697.1
2.58-2.73.50.09660080.9860.0590.1133.5897.5
2.7-2.843.50.08760060.9880.0530.1033.89897.9
2.84-3.023.50.08260130.9890.050.0974.24998
3.02-3.253.60.07660390.9910.0460.0894.78898.5
3.25-3.583.70.06760630.9920.040.0785.23198.9
3.58-4.093.70.06160530.9930.0360.0715.98199
4.09-5.163.70.05761050.9940.0340.0676.11899
5.16-503.50.06258590.990.0390.0736.40195.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→33.61 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.203 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.136
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1965 5902 5 %RANDOM
Rwork0.1459 ---
obs0.1484 113299 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 95.84 Å2 / Biso mean: 23.485 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.46 Å20.94 Å2
2--0.62 Å2-0.1 Å2
3----1.3 Å2
Refinement stepCycle: final / Resolution: 1.9→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12800 0 136 1368 14304
Biso mean--29.21 34.92 -
Num. residues----1760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01313140
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712512
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.6417868
X-RAY DIFFRACTIONr_angle_other_deg1.3991.5728848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6551756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60221.429616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.229151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.60715104
X-RAY DIFFRACTIONr_chiral_restr0.080.21784
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022676
LS refinement shellResolution: 1.901→1.95 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 409 -
Rwork0.196 7907 -
all-8316 -
obs--91.84 %

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