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- PDB-1ama: DOMAIN CLOSURE IN MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE -

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Basic information

Entry
Database: PDB / ID: 1ama
TitleDOMAIN CLOSURE IN MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsTRANSFERASE(AMINOTRANSFERASE)
Function / homology
Function and homology information


Amino acid metabolism / Gluconeogenesis / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity ...Amino acid metabolism / Gluconeogenesis / aspartate catabolic process / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / 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-PLA / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsVincent, M.G. / Genovesio-Taverne, J.-C. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: Domain closure in mitochondrial aspartate aminotransferase.
Authors: McPhalen, C.A. / Vincent, M.G. / Picot, D. / Jansonius, J.N. / Lesk, A.M. / Chothia, C.
#1: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Structural Basis for Catalysis by Aspartate Aminotransferase
Authors: Jansonius, J.N. / Vincent, M.G.
History
DepositionFeb 5, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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)45,3712
Polymers44,9921
Non-polymers3781
Water5,621312
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7424
Polymers89,9852
Non-polymers7572
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7050 Å2
ΔGint-22 kcal/mol
Surface area29530 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
Atom site foot note1: CIS PROLINE - PRO 138 / 2: CIS PROLINE - PRO 195
3: RESIDUE 411 REPRESENTS THE ALPHA-METHYL ASPARTATE-PLP COMPLEX AND HAS BEEN GIVEN THE NAME AMA.
Components on special symmetry positions
IDModelComponents
11A-641-

HOH

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / Aspartate transaminase


Mass: 44992.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: HEART / Production host: unidentified (others) / References: UniProt: P00508, aspartate transaminase
#2: Chemical ChemComp-PLA / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID / N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE


Mass: 378.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N2O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: AATM_CHICK SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 47 PRO 47 CAREFUL EXAMINATION OF ELECTRON DENSITY FOR RESIDUE 47 IN THIS AND OTHER STUDIES ON ASPARTATE AMINOTRANSFERASE INDICATE THAT IT WOULD BE EXTREMELY IMPROBABLE THAT ANYTHING OTHER THAN A PROLINE RESIDUE COULD BE MODELLED IN THE MAP.

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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 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
PROLSQrefinement
TNTrefinement
RefinementResolution: 2.3→10 Å / σ(F): 0
Details: THE MOLECULE IS AN ALPHA2 DIMER. THE SUBUNITS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD ROTATION AXIS. THE RESIDUES ARE NUMBERED FROM 3 TO 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE ...Details: THE MOLECULE IS AN ALPHA2 DIMER. THE SUBUNITS ARE RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD ROTATION AXIS. THE RESIDUES ARE NUMBERED FROM 3 TO 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE LONGER SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE (SEE U. GRAF-HAUSNER, K.J.WILSON AND P.CHRISTEN (1983), J.BIOL.CHEM. 258, 8813-8826). ONE MOLECULE OF THE ALPHA-METHYL ASPARTATE-PLP COMPLEX (AMA) IS BOUND (NON-COVALENTLY) PER SUBUNIT.
RfactorNum. reflection
obs0.159 17538
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 25 312 3498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.017
X-RAY DIFFRACTIONp_angle_d3.46
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 10 Å / Num. reflection all: 17538 / σ(F): 0 / Rfactor all: 0.159
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.46

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