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- PDB-21ft: GABA aminotransferase from Arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 21ft
TitleGABA aminotransferase from Arabidopsis thaliana
ComponentsGamma-aminobutyrate transaminase POP2, mitochondrial
KeywordsPLANT PROTEIN / GABA
Function / homology
Function and homology information


4-aminobutyrate-pyruvate transaminase / adaxial/abaxial axis specification / beta-alanine catabolic process / 4-aminobutyrate:pyruvate transaminase activity / fruit development / GABA shunt / pollen tube guidance / shoot system development / pollen tube adhesion / pollen tube growth ...4-aminobutyrate-pyruvate transaminase / adaxial/abaxial axis specification / beta-alanine catabolic process / 4-aminobutyrate:pyruvate transaminase activity / fruit development / GABA shunt / pollen tube guidance / shoot system development / pollen tube adhesion / pollen tube growth / sucrose metabolic process / : / GABA catabolic process / succinate metabolic process / leaf development / S-adenosyl-L-methionine:8-amino-7-oxononanoate transaminase activity / root development / glutamate metabolic process / inositol metabolic process / biotin biosynthetic process / plant-type vacuole / L-glutamine metabolic process / response to alcohol / cobalt ion binding / response to salt stress / pyridoxal phosphate binding / Golgi apparatus / mitochondrion / zinc ion binding / cytosol
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Gamma-aminobutyrate transaminase POP2, mitochondrial
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOkoda, N. / Okuda, S. / Tsutsumi, K. / Sano, K. / Kobata, K. / Nagata, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Not funded Japan
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2026
Title: Crystal structure of the plant GABA aminotransferase AtGABA-T from Arabidopsis thaliana.
Authors: Okoda, N. / Okuda, S. / Tsutsumi, K. / Itoh, H. / Okamoto, K. / Kawakami, H. / Sano, K. / Kobata, K. / Nagata, K.
History
DepositionDec 12, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyrate transaminase POP2, mitochondrial
B: Gamma-aminobutyrate transaminase POP2, mitochondrial
C: Gamma-aminobutyrate transaminase POP2, mitochondrial
D: Gamma-aminobutyrate transaminase POP2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)208,6664
Polymers208,6664
Non-polymers00
Water20,7171150
1
A: Gamma-aminobutyrate transaminase POP2, mitochondrial
B: Gamma-aminobutyrate transaminase POP2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)104,3332
Polymers104,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-78 kcal/mol
Surface area29450 Å2
MethodPISA
2
C: Gamma-aminobutyrate transaminase POP2, mitochondrial
D: Gamma-aminobutyrate transaminase POP2, mitochondrial


Theoretical massNumber of molelcules
Total (without water)104,3332
Polymers104,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-77 kcal/mol
Surface area29470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.178, 78.268, 93.216
Angle α, β, γ (deg.)96.76, 88.88, 106.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Gamma-aminobutyrate transaminase POP2, mitochondrial / AtGABA-T / Gamma-aminobutyric acid aminotransferase 1 / Protein HEXENAL RESPONSE 1 / Protein POLLEN- ...AtGABA-T / Gamma-aminobutyric acid aminotransferase 1 / Protein HEXENAL RESPONSE 1 / Protein POLLEN-PISTIL INCOMPATIBILITY 2 / AtPOP2


Mass: 52166.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: POP2, GABA-T, GABAT1, HER1, At3g22200, MKA23.11 / Production host: Escherichia coli KRX (bacteria)
References: UniProt: Q94CE5, 4-aminobutyrate-pyruvate transaminase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.899995 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.899995 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 110288 / % possible obs: 96.8 % / Redundancy: 3.56 % / CC1/2: 0.991 / Net I/σ(I): 10.79
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 17782 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.21_5207: ???refinement
HKL-2000data reduction
XDSdata scaling
HKL-2000data collection
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→41.58 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1984 5329 -
Rwork0.1531 104934 -
obs0.1553 110263 96.81 %
Refinement stepCycle: LAST / Resolution: 2→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14081 0 0 1150 15231
Refinement TLS params.Origin x: -0.3889 Å / Origin y: 0.1841 Å / Origin z: 0.3102 Å
111213212223313233
T0.0178 Å20.0029 Å2-0.0087 Å2-0.0368 Å20.0055 Å2--0.0464 Å2
L0.0486 °2-0.0187 °2-0.0782 °2-0.1045 °20.0617 °2--0.1707 °2
S-0.0039 Å °-0.0138 Å °0.0081 Å °0.0032 Å °0.0073 Å °-0.0096 Å °0.0325 Å °0.013 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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