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- PDB-1tat: CRYSTALLINE MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE EXISTS IN ON... -

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Basic information

Entry
Database: PDB / ID: 1tat
TitleCRYSTALLINE MITOCHONDRIAL ASPARTATE AMINOTRANSFERASE EXISTS IN ONLY TWO CONFORMATIONS
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE
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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHohenester, E. / Jansonius, J.N.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystalline mitochondrial aspartate aminotransferase exists in only two conformations.
Authors: Hohenester, E. / Jansonius, J.N.
#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 4, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Mar 26, 2025Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4794
Polymers89,9852
Non-polymers4942
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-29 kcal/mol
Surface area29930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.500, 89.600, 144.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SER A 3 - SER A 4 OMEGA =357.82 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: CIS PROLINE - PRO A 138 / 3: CIS PROLINE - PRO A 195 / 4: CIS PROLINE - PRO B 138 / 5: CIS PROLINE - PRO B 195
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9999, -0.0095, -0.0072), (-0.008, 0.0803, 0.9967), (-0.0089, 0.9967, -0.0803)
Vector: 49.69, 18.52, -19.77)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW DESCRIBES THE NON-CRYSTALLOGRAPHIC TWO-FOLD AXIS OF THE DIMER. IT WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THE TWO-FOLD AXIS OF THE DIMER LIES IN THE BC-PLANE. THE ANGLE BETWEEN THE TWO-FOLD AXIS AND THE C-AXIS IS 45 DEGREES.

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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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
Has protein modificationN
Nonpolymer detailsTHE MALEATE MOLECULES THAT ARE BOUND TO THE ACTIVE SITES A AND B HAVE NOT BEEN INCLUDED IN THE MODEL.
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 A 47 SER 47 PRO B 47

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.85 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119-21 %(w/v)PEG40001reservoir
210-12 mg/mlasparatate aminotransferase1drop
31

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 18194 / % possible obs: 97 % / Num. measured all: 65983 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.08 Å / % possible obs: 88 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 3→15 Å / Rfactor obs: 0.15 / σ(F): 0
Details: ATOMS OF SIDE CHAINS THAT ARE NOT WELL DEFINED BY THE ELECTRON DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 30 0 6352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg3.1
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_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor all: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_plane_restr0.011

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