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- PDB-1oxp: ASPARTATE AMINOTRANSFERASE, H-ASP COMPLEX, CLOSED CONFORMATION -

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Basic information

Entry
Database: PDB / ID: 1oxp
TitleASPARTATE AMINOTRANSFERASE, H-ASP COMPLEX, CLOSED CONFORMATION
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / VITAMIN B6 / HYDROXYLAMINE DERIVED INHIBITORS
Function / homology
Function and homology information


Amino acid metabolism / Gluconeogenesis / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / 2-oxoglutarate metabolic process ...Amino acid metabolism / Gluconeogenesis / kynurenine-oxoglutarate transaminase / kynurenine-oxoglutarate transaminase activity / aspartate metabolic process / glutamate metabolic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / 2-oxoglutarate metabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / mitochondrial matrix / protein homodimerization activity / mitochondrion / 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 / 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
4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHohenester, E. / Schirmer, T. / Jansonius, J.N.
Citation
Journal: Eur.J.Biochem. / Year: 1996
Title: Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase.
Authors: Markovic-Housley, Z. / Schirmer, T. / Hohenester, E. / Khomutov, A.R. / Khomutov, R.M. / Karpeisky, M.Y. / Sandmeier, E. / Christen, P. / Jansonius, J.N.
#1: Journal: To be Published
Title: Spatial Structure of Mitochondrial Aspartate Aminotransferase
Authors: Jansonius, J.N. / Eichele, G. / Ford, G.C. / Picot, D. / Thaller, C. / Vincent, M.G.
History
DepositionDec 23, 1995Processing site: BNL
Revision 1.0Jun 10, 1996Provider: 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: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3152
Polymers44,9921
Non-polymers3221
Water3,873215
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6294
Polymers89,9852
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8590 Å2
ΔGint-31 kcal/mol
Surface area29360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)69.500, 91.550, 128.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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-IK2 / 4'-DEOXY-4'-ACETYLYAMINO-PYRIDOXAL-5'-PHOSPHATE


Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES IN EACH SUBUNIT ARE NUMBERED FROM 3 TO 410, ACCORDING TO A SEQUENCE ALIGNMENT WITH THE ...THE RESIDUES IN EACH SUBUNIT 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).

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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: 45.77 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
280 mMD,L-methyl aspartate1drop
320 mMsodium phosphate1drop
48-14 %(w/v)PEG1drop
516-28 %(w/v)PEG1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1990
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 11781 / % possible obs: 81.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.057

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Processing

Software
NameClassification
PROLSQrefinement
MADNESdata reduction
RefinementResolution: 2.5→8 Å / Num. reflection obs: 11411 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 21 215 3397
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0560.04
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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