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- PDB-9aat: X-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOC... -

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Basic information

Entry
Database: PDB / ID: 9aat
TitleX-RAY STRUCTURE REFINEMENT AND COMPARISON OF THREE FORMS OF MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE
ComponentsASPARTATE AMINOTRANSFERASE
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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsMcphalen, C.A. / Vincent, M.G. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1992
Title: X-ray structure refinement and comparison of three forms of mitochondrial aspartate aminotransferase.
Authors: McPhalen, C.A. / Vincent, M.G. / Jansonius, J.N.
#1: Journal: Eur.J.Biochem. / Year: 1991
Title: The Open(Slash)Closed Conformational Equilibrium of Aspartate Aminotransferase: Studies in the Crystalline State and with a Fluorescent Probe in Solution
Authors: Picot, D. / Sandmeier, E. / Thaller, C. / Vincent, M.G. / Christen, P. / Jansonius, J.N.
#2: Journal: J.Mol.Biol. / Year: 1984
Title: Mechanism of Action of Aspartate Aminotransferase Proposed on the Basis of its Spatial Structure
Authors: Kirsch, J.F. / Eichele, G. / Ford, G.C. / Vincent, M.G. / Jansonius, J.N. / Gehring, H. / Christen, P.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980
Title: Three-Dimensional Structure of a Pyridoxal-Phosphate-Dependent Enzyme, Mitochondrial Aspartate Aminotransferase
Authors: Ford, G.C. / Eichele, G. / Jansonius, J.N.
History
DepositionDec 2, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 1.4Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4814
Polymers89,9852
Non-polymers4962
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-28 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.670, 58.660, 75.790
Angle α, β, γ (deg.)85.20, 109.30, 115.70
Int Tables number1
Space group name H-MP1
Atom site foot note1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 / 3: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195
5: THE NON-COVALENTLY BOUND COFACTOR PMP HAS BEEN GIVEN THE RESIDUE NUMBER 411 FOR CHAINS *A* AND *B*.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92423, 0.34441, -0.16487), (0.35371, 0.60953, -0.70948), (-0.14386, -0.71404, -0.68517)
Vector: 20.32, 16.939, 48.305)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*, WITH AN RMSD=0.73. THE MOLECULE IS AN ALPHA2 DIMER. THE SUBUNITS ARE RELATED BY A LOCAL TWO-FOLD ROTATION AXIS. THEY ARE DISTINGUISHED BY CHAIN IDENTIFIERS A AND B, RESPECTIVELY. 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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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 44992.484 Da / Num. of mol.: 2
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 620 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsONE MOLECULE OF THE COFACTOR PYRIDOXAMINE PHOSPHATE (PMP) IS BOUND (NON-COVALENTLY) PER SUBUNIT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMphosphate1drop
320 %PEG40001drop
420 mMphosphate1reservoir
520 %PEG40001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 38963

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→10 Å / σ(F): 0 /
RfactorNum. reflection
obs0.131 38963
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 32 620 6974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.007
X-RAY DIFFRACTIONp_angle_d
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 obs: 0.131
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 5.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.020.028
X-RAY DIFFRACTIONp_dihedral_angle_d2.51.4
X-RAY DIFFRACTIONp_planar_d0.020.023
X-RAY DIFFRACTIONp_plane_restr0.010.007
X-RAY DIFFRACTIONp_chiral_restr0.20.21
X-RAY DIFFRACTIONp_mcbond_it44.2
X-RAY DIFFRACTIONp_scbond_it89.2
X-RAY DIFFRACTIONp_mcangle_it65.4
X-RAY DIFFRACTIONp_scangle_it1212.4

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