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- PDB-1ivr: STRUCTURE OF ASPARTATE AMINOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1ivr
TitleSTRUCTURE OF ASPARTATE AMINOTRANSFERASE
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / ASPARTATE AMINOTRANSFERASE / ERYTHRO-BETA-HYDROXYASPARTATE / CARBINOLAMINE
Function / homology
Function and homology information


Amino acid metabolism / Gluconeogenesis / L-aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process ...Amino acid metabolism / Gluconeogenesis / L-aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 2-oxoglutarate metabolic process / biosynthetic process / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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-CBA / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGraf Von Stosch, A.
Citation
Journal: Biochemistry / Year: 1996
Title: Aspartate aminotransferase complexed with erythro-beta-hydroxyaspartate: crystallographic and spectroscopic identification of the carbinolamine intermediate.
Authors: von Stosch, A.G.
#1: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Structural Basis for Catalysis by Aspartate Aminotransferase
Authors: Jansonius, J.N. / Vincent, M.G.
History
DepositionOct 11, 1996Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3892
Polymers44,9921
Non-polymers3961
Water5,531307
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7774
Polymers89,9852
Non-polymers7922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8640 Å2
ΔGint-31 kcal/mol
Surface area29430 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.700, 91.400, 128.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A DIMER. THIS ENTRY CONTAINS ONLY ONE HALF OF THE ASYMMETRIC UNIT.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 44992.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Organelle: MITOCHONDRIA / Production host: unidentified (others) / References: UniProt: P00508, aspartate transaminase
#2: Chemical ChemComp-CBA / N-PYRIDOXYL-2,3-DIHYDROXYASPARTIC ACID-5-MONOPHOSPHATE


Mass: 396.244 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17N2O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE ERYTHRO-BETA-HYDROXYASPARTATE MOLECULE THAT IS BOUND TO THE ACTIVE SITES A AND B HAS BEEN ...THE ERYTHRO-BETA-HYDROXYASPARTATE MOLECULE THAT IS BOUND TO THE ACTIVE SITES A AND B HAS BEEN INCLUDED IN THE MODEL.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
250 mMmaleate1drop
310 mMsodium phosphate1drop
48.5-9.5 %(w/v)PEG40001drop
50.04 Msodium chloride1drop
617-19 %(w/v)PEG40001reservoir
70.75 Msodium chloride1reservoir
820 mMsodium phosphate1reservoir

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Data collection

DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Jun 30, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRmerge(I) obs: 0.081

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Processing

Software
NameClassification
TNTrefinement
PROLSQrefinement
RefinementResolution: 2.4→10 Å / σ(F): 1
Details: PROLSQ (KONNERT,HENDRICKSON) ALSO WAS USED. ATOMS OF SIDE CHAINS THAT ARE NOT WELL DEFINED BY THE ELECTRON DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. ATOMS OF SIDE CHAINS THAT ARE NOT ...Details: PROLSQ (KONNERT,HENDRICKSON) ALSO WAS USED. ATOMS OF SIDE CHAINS THAT ARE NOT WELL DEFINED BY THE ELECTRON DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. ATOMS OF SIDE CHAINS THAT ARE NOT WELL DEFINED BY THE ELECTRON DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. AS SHOWN BY MCPHALIN ET AL. J. MOL. BIOL. 225, 495-517, 1992, RESIDUES SER 104, SER 123, TYR 255, AND SER 288 LIE WITHIN DISTORTED REGIONS.
RfactorNum. reflection
Rwork0.153 -
obs-13631
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 26 307 3494
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.024
X-RAY DIFFRACTIONt_angle_deg3.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.016
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.153
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_planar_d0.050.078
X-RAY DIFFRACTIONt_plane_restr0.020.016

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