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- PDB-1ohw: 4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-vinyl GABA -

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Basic information

Entry
Database: PDB / ID: 1ohw
Title4-AMINOBUTYRATE-AMINOTRANSFERASE inactivated by gamma-vinyl GABA
Components4-AMINOBUTYRATE AMINOTRANSFERASE
KeywordsTRANSFERASE / PLP-DEPENDENT ENZYME / AMINOTRANSFERASE / 4- AMINOBUTYRIC ACID / ANTIEPILEPTIC DRUG TARGET / VIGABATRIN PYRIDOXAL PHOSPHATE / NEUROTRANSMITTER DEGRADATION / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine ...(S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / (S)-3-amino-2-methylpropionate transaminase activity / Degradation of GABA / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / 4-aminobutyrate transaminase activity / gamma-aminobutyric acid catabolic process / behavioral response to cocaine / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / identical protein binding / metal ion binding / cytosol
Similarity search - Function
4-aminobutyrate aminotransferase, eukaryotic / : / 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 ...4-aminobutyrate aminotransferase, eukaryotic / : / 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
FE2/S2 (INORGANIC) CLUSTER / PYRIDOXAL-5'-PHOSPHATE / 4-AMINO HEXANOIC ACID / 4-aminobutyrate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.3 Å
AuthorsStorici, P. / Schirmer, T.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Structures of {Gamma}-Aminobutyric Acid (Gaba) Aminotransferase, a Pyridoxal 5'-Phosphate, and [2Fe-2S] Cluster-Containing Enzyme, Complexed with {Gamma}-Ethynyl-Gaba and with the Antiepilepsy Drug Vigabatrin
Authors: Storici, P. / De Biase, D. / Bossa, F. / Bruno, S. / Mozzarelli, A. / Peneff, C. / Silverman, R. / Schirmer, T.
#1: Journal: Biochemistry / Year: 1999
Title: Crystal Structure of Gaba-Aminotransferase, a Target for Antiepileptic Drug Therapy
Authors: Storici, P. / Capitani, G. / De Biase, D. / Moser, M. / John, R.A. / Jansonius, J.N. / Schirmer, T.
History
DepositionJun 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)215,34114
Polymers213,4764
Non-polymers1,86510
Water12,899716
1
A: 4-AMINOBUTYRATE AMINOTRANSFERASE
B: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6707
Polymers106,7382
Non-polymers9325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: 4-AMINOBUTYRATE AMINOTRANSFERASE
D: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6707
Polymers106,7382
Non-polymers9325
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.660, 226.712, 71.366
Angle α, β, γ (deg.)90.00, 108.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A13 - 20
2111B13 - 20
3111C13 - 20
4111D13 - 20
1211A22 - 33
2211B22 - 33
3211C22 - 33
4211D22 - 33
1311A38 - 51
2311B38 - 51
3311C38 - 51
4311D38 - 51
1411A55 - 133
2411B55 - 133
3411C55 - 133
4411D55 - 133
1511A140 - 150
2511B140 - 150
3511C140 - 150
4511D140 - 150
1611A162 - 220
2611B162 - 220
3611C162 - 220
4611D162 - 220
1711A224 - 328
2711B224 - 328
3711C224 - 328
4711D224 - 328
1811A340 - 450
2811B340 - 450
3811C340 - 450
4811D340 - 450

NCS oper:
IDCodeMatrixVector
1given(-0.421, 0.9066, -0.0278), (0.9068, 0.42, -0.0365), (-0.0214, -0.0406, -0.9989)27.1736, -15.6296, 59.5179
2given(0.2282, 0.4668, 0.8544), (-0.9628, -0.0224, 0.2693), (0.1449, -0.8841, 0.4443)0.9494, 61.245, 51.5929
3given(0.311, 0.3717, -0.8747), (0.3801, -0.8922, -0.244), (-0.8711, -0.2566, -0.4187)50.6045, 51.6099, 95.9318

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Components

#1: Protein
4-AMINOBUTYRATE AMINOTRANSFERASE / MITOCHONDRIAL PRECURSOR / GAMMA-AMINO-N-BUTYRATE TRANSAMINASE / GABA TRANSAMINASE / GABA ...MITOCHONDRIAL PRECURSOR / GAMMA-AMINO-N-BUTYRATE TRANSAMINASE / GABA TRANSAMINASE / GABA AMINOTRANSFERASE / GABA-AT / GABA-T / ABAT / GABAT


Mass: 53368.996 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: AFTER REACTION WITH 4-AMINO-5-HEXENOIC ACID (GAMMA-VINYL GABA, VIGABATRIN) THE FRAGMENT VIG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE ...Details: AFTER REACTION WITH 4-AMINO-5-HEXENOIC ACID (GAMMA-VINYL GABA, VIGABATRIN) THE FRAGMENT VIG HAS BEEN GENERATED WHICH IS COVALENTLY ATTACHED VIA A DOUBLE BOND TO C4A OF PLP AND VIA A SINGLE BOND TO NZ OF THE ACTIVE SITE LYS 329
Source: (natural) SUS SCROFA (pig) / Organ: LIVER
References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-VIG / 4-AMINO HEXANOIC ACID


Mass: 131.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO2
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 716 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 4-AMINOBUTANOATE + 2-OXOGLUTARATE = SUCCINATE SEMIALDEHYDE + L-GLUTAMATE.

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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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growpH: 5.7 / Details: pH 5.70
Crystal grow
*PLUS
pH: 5.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-14 mg/mlprotein1drop
240 mMsodium acetate1droppH5.4
316-18 %PEG40001reservoir
40-10 %glycerol1reservoir
550 mMsodium cacodylate1reservoirpH6.0
61 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.984
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 88767 / % possible obs: 96.1 % / Redundancy: 2.22 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.6779
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.18 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 4.14 / % possible all: 96.7
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.073

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.423 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.36 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4412 5 %RANDOM
Rwork0.188 ---
obs0.19 84308 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-1.47 Å2
2---0.5 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14403 0 104 716 15223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02114872
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213318
X-RAY DIFFRACTIONr_angle_refined_deg1.1571.95520105
X-RAY DIFFRACTIONr_angle_other_deg0.847330961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54951840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0710.22160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216563
X-RAY DIFFRACTIONr_gen_planes_other0.0180.023090
X-RAY DIFFRACTIONr_nbd_refined0.1980.23085
X-RAY DIFFRACTIONr_nbd_other0.240.214966
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.27696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2714
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4040.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.340.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2431.59204
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.433214800
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.86335668
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.294.55305
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5972 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.060.05
2Btight positional0.060.05
3Ctight positional0.060.05
4Dtight positional0.050.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.060.5
4Dtight thermal0.060.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.28 330
Rwork0.226 6174
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6925-0.1320.14921.0509-0.10590.9614-0.0238-0.0044-0.03120.0323-0.00970.13540.0395-0.05110.03350.06170.0429-0.00090.0495-0.04260.08915.6683.53421.259
20.650.09720.40930.84780.27331.23850.0338-0.0532-0.05530.18660.0072-0.07670.2140.1229-0.0410.17370.0844-0.02140.0868-0.02690.083126.843-9.49837.377
31.014-0.38310.14740.9283-0.05650.80220.06060.2054-0.0244-0.1178-0.07560.09-0.082-0.00070.0150.0402-0.0072-0.00710.0724-0.01310.054822.01361.14258.271
41.1979-0.37760.10860.5563-0.02830.64250.0199-0.0459-0.08450.0328-0.002-0.00750.03650.0202-0.01790.0235-0.015-0.00050.0141-0.01240.048734.56845.31380.023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 471
2X-RAY DIFFRACTION2B11 - 471
3X-RAY DIFFRACTION3C11 - 471
4X-RAY DIFFRACTION4D11 - 471
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.224 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.2

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