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- PDB-1aat: OXOGLUTARATE-INDUCED CONFORMATIONAL CHANGES IN CYTOSOLIC ASPARTAT... -

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Entry
Database: PDB / ID: 1aat
TitleOXOGLUTARATE-INDUCED CONFORMATIONAL CHANGES IN CYTOSOLIC ASPARTATE AMINOTRANSFERASE
ComponentsCYTOSOLIC ASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE
Function / homology
Function and homology information


Amino acid metabolism / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / aspartate biosynthetic process / Gluconeogenesis / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process ...Amino acid metabolism / L-glutamate catabolic process to aspartate / cysteine transaminase / phosphatidylserine decarboxylase activity / L-cysteine transaminase activity / aspartate biosynthetic process / Gluconeogenesis / malate-aspartate shuttle / L-aspartate catabolic process / glycerol biosynthetic process / aspartate metabolic process / glutamate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / oxaloacetate metabolic process / 2-oxoglutarate metabolic process / fatty acid homeostasis / Notch signaling pathway / response to glucocorticoid / gluconeogenesis / cellular response to insulin stimulus / pyridoxal phosphate binding / cytosol
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Aspartate aminotransferase, cytoplasmic
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsHarutyunyan, E.G. / Malashkevich, V.N.
Citation
Journal: DOKL.AKAD.NAUK SSSR / Year: 1982
Title: Conformational changes in cytosol aspartate aminotransferase induced by oxoglutarate
Authors: Malashkevich, V.N. / Kochkina, V.M. / Torchinskii, I.u.M. / Arutiunian, E.G.
#1: Journal: Prog.Clin.Biol.Res. / Year: 1982
Title: Aspartate Aminotranferase from Chicken Heart Cytosol. Three-Dimensional Structure and Coenzyme Reorientations in the Active Site
Authors: Torchinsky, Yu.M. / Harutyunyan, E.G. / Malashkevich, V.N. / Kochkina, V.M. / Makarov, V.L. / Braunstein, A.E.
#2: Journal: FEBS Lett. / Year: 1982
Title: Three-Dimensional Structure at 3.2 Angstroms Resolution of the Complex of Cytosolic Aspartate Aminotransferase from Chicken Heart with 2-Oxoglutarate
Authors: Harutyunyan, E.G. / Malashkevich, V.N. / Tersyan, S.S. / Kochkina, V.M. / Torchinsky, Yu.M. / Braunstein, A.E.
#3: Journal: FEBS Lett. / Year: 1979
Title: Primary Structure of Cytoplasmic Aspartate Aminotransferase from Chicken Heart and its Homology with Pig Heart Isoenzymes
Authors: Shlyapnikov, S.V. / Myasnikov, A.N. / Severin, E.S. / Myagkova, M.A. / Torchinsky, Yu.M. / Braunstein, A.E.
History
DepositionApr 23, 1982Processing site: BNL
Revision 1.0Oct 21, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 31, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_PDB_matrix / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOSOLIC ASPARTATE AMINOTRANSFERASE
B: CYTOSOLIC ASPARTATE AMINOTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)91,7402
Polymers91,7402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.700, 118.100, 124.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.224554, -0.974529, 0.028477), (-0.97521, 0.225579, -0.035813), (-0.027911, 0.035077, -1.001025)
Vector: 140.16586, 114.75697, 110.3668)

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Components

#1: Protein CYTOSOLIC ASPARTATE AMINOTRANSFERASE / Coordinate model: Cα atoms only


Mass: 45869.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00504, aspartate transaminase
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THE SEQUENCE HOMOLOGY WITH PIG CYTOSOLIC ASPARTATE ...THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE HOMOLOGY WITH PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE. THIS STRUCTURE IS SIMILAR TO CHICKEN HEART MITOCHONDRIAL AND PIG HEART CYTOSOLIC ASPARTATE AMINOTRANSFERASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.02 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms822 0 0 0 822

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