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- PDB-1ohv: 4-AMINOBUTYRATE-AMINOTRANSFERASE FROM PIG -

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Basic information

Entry
Database: PDB / ID: 1ohv
Title4-AMINOBUTYRATE-AMINOTRANSFERASE FROM PIG
Components4-AMINOBUTYRATE AMINOTRANSFERASE
KeywordsTRANSFERASE / PLP-DEPENDENT ENZYME / AMINOTRANSFERASE / 4- AMINOBUTYRIC ACID / ANTIEPILEPTIC DRUG TARGET
Function / homology
Function and homology information


4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / Degradation of GABA / (S)-3-amino-2-methylpropionate transaminase activity / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid catabolic process / nervous system process / 2 iron, 2 sulfur cluster binding ...4-aminobutyrate transaminase complex / succinate-semialdehyde dehydrogenase binding / Degradation of GABA / (S)-3-amino-2-methylpropionate transaminase activity / (S)-3-amino-2-methylpropionate transaminase / 4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid catabolic process / nervous system process / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / metal ion binding / identical protein 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
ACETATE ION / FE2/S2 (INORGANIC) CLUSTER / PYRIDOXAL-5'-PHOSPHATE / 4-aminobutyrate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 2, 2003Deposition site: PDBE / Processing site: PDBE
SupersessionJun 3, 2003ID: 1GTX
Revision 1.0Oct 16, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 4-AMINOBUTYRATE AMINOTRANSFERASE
B: 4-AMINOBUTYRATE AMINOTRANSFERASE
C: 4-AMINOBUTYRATE AMINOTRANSFERASE
D: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,05214
Polymers213,4764
Non-polymers1,57610
Water11,403633
1
A: 4-AMINOBUTYRATE AMINOTRANSFERASE
B: 4-AMINOBUTYRATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,5267
Polymers106,7382
Non-polymers7885
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)107,5267
Polymers106,7382
Non-polymers7885
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)68.597, 225.045, 70.349
Angle α, β, γ (deg.)90.00, 108.39, 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 - 150
2411B55 - 150
3411C55 - 150
4411D55 - 150
1511A170 - 220
2511B170 - 220
3511C170 - 220
4511D170 - 220
1611A224 - 250
2611B224 - 250
3611C224 - 250
4611D224 - 250
1711A260 - 328
2711B260 - 328
3711C260 - 328
4711D260 - 328
1811A340 - 370
2811B340 - 370
3811C340 - 370
4811D340 - 370
1911A375 - 450
2911B375 - 450
3911C375 - 450
4911D375 - 450
11011A500
21011B500
31011C500
41011D500
11111A800
21111B800
31111C800
41111D800

NCS oper:
IDCodeMatrixVector
1given(-0.423, 0.9057, -0.0284), (0.9058, 0.4217, -0.0418), (-0.0258, -0.0434, -0.9987)26.599, -15.2273, 58.9378
2given(0.2282, 0.4651, 0.8553), (-0.963, -0.0218, 0.2687), (0.1436, -0.885, 0.4429)0.8697, 60.9876, 51.1982
3given(0.3036, 0.3701, -0.878), (0.3829, -0.8912, -0.2433), (-0.8725, -0.2623, -0.4123)50.1957, 51.5296, 94.6709

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Components

#1: Protein
4-AMINOBUTYRATE AMINOTRANSFERASE / GAMMA-AMINO-N-BUTYRATE TRANSAMINASE / GABA TRANSAMINASE / GABA AMINOTRANSFERASE / GABA-AT / GABA-T


Mass: 53368.996 Da / Num. of mol.: 4 / Fragment: RESIDUES 29-500 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: LIVER
References: UniProt: P80147, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


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


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.41 Å3/Da / Density % sol: 49.04 %
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: ESRF / Type: ESRF / Wavelength: 0.9
DetectorDetector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→28.2 Å / Num. obs: 39236 / % possible obs: 90.8 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 5.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.25 / % possible all: 93
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 80297 / % possible obs: 90 % / Redundancy: 2 % / Rmerge(I) obs: 0.085

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GTX

1gtx
PDB Unreleased entry


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.919 / SU ML: 0.168 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 4018 5 %RANDOM
Rwork0.188 ---
obs-76236 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 18.17 Å2
Baniso -1Baniso -2Baniso -3
1--2.77 Å20 Å2-0.71 Å2
2--1.1 Å20 Å2
3---1.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14363 0 84 633 15080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02114809
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213258
X-RAY DIFFRACTIONr_angle_refined_deg1.2961.95320026
X-RAY DIFFRACTIONr_angle_other_deg0.743330805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.70431840
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.888152611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.22160
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216539
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023078
X-RAY DIFFRACTIONr_nbd_refined0.2310.33619
X-RAY DIFFRACTIONr_nbd_other0.2040.313593
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.51172
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1430.57
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.344
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.381
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4550.519
X-RAY DIFFRACTIONr_symmetry_hbond_other0.2750.51
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4051.59196
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.82214768
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.31235613
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.314.55258
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: 5698 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.020.05
2Btight positional0.020.05
3Ctight positional0.020.05
4Dtight positional0.020.05
1Atight thermal0.050.5
2Btight thermal0.050.5
3Ctight thermal0.050.5
4Dtight thermal0.050.5
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 317
Rwork0.218 5752
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)
10.3041-0.10080.12140.36430.00360.3374-0.0102-0.0019-0.0310.0167-0.0180.0663-0.0005-0.00240.02820.05440.01990.01050.0604-0.02630.07935.743.57621.325
20.2614-0.03150.20540.22790.0980.4706-0.0043-0.0259-0.04740.05390.0063-0.02390.09020.0624-0.0020.08210.04050.00420.0858-0.02050.087326.827-9.4137.311
30.5432-0.14970.11020.468-0.04390.25140.02330.13090.0079-0.0356-0.01740.0478-0.01830.023-0.00590.0458-0.0116-0.00880.08420.01090.063522.08461.14858.304
40.7054-0.25090.14610.205-0.06140.20870.0156-0.0504-0.0391-0.00280.01680.01450.0148-0.0163-0.03240.0325-0.0129-0.00110.05870.00150.063634.54245.36279.947
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 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.1

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