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

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Basic information

Entry
Database: PDB / ID: 1tas
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
Chem-PLA / Aspartate aminotransferase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2.8 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: Eur.J.Biochem. / Year: 1991
Title: The Open(Slash)Closed Equilibrium of Aspartate Aminotransferase
Authors: Picot, D. / Sandmeier, E. / Thaller, C. / Vincent, M.G. / Christen, P. / Jansonius, J.N.
#2: Journal: Biological Macromolecules and Assemblies / Year: 1987
Title: Structural Basis for Catalysis by Aspartate Aminotransferase
Authors: Jansonius, J.N. / Vincent, M.G.
#3: Journal: J.Mol.Biol. / Year: 1981
Title: Repeated Seeding Technique for Growing Large Single Crystals of Proteins
Authors: Thaller, C. / Weaver, L.H. / Eichele, G. / Wilson, E. / Karlsson, R. / Jansonius, J.N.
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: 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 1.4Feb 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 / pdbx_unobs_or_zero_occ_residues / 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)90,7424
Polymers89,9852
Non-polymers7572
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-24 kcal/mol
Surface area29910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.400, 52.400, 136.900
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number4
Space group name H-MP1211
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
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7723, -0.592, -0.2305), (-0.5912, 0.5368, 0.602), (-0.2326, 0.6012, -0.7645)
Vector: 81.81, -35.1, 170.08)
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*.

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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-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.: 2 / Source method: obtained synthetically / Formula: C13H19N2O9P
Nonpolymer detailsPLA IS PYRIDOXAL-5'-PHOSPHATE BOUND TO ALPHA-METHYLASPARTIC ACID.
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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
280 mMD,L-2-methyl aspartate1drop
320 mMsodium phosphate1droppH7.5
48-14 %(w/v)PEG1drop
516-28 %(w/v)PEG1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 17636 / % possible obs: 87.9 % / Num. measured all: 44737 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.87 Å / % possible obs: 83.7 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.8→15 Å / Rfactor obs: 0.16 / 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: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6322 0 50 0 6372
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.8
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
Refinement
*PLUS
Num. reflection obs: 6096
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_plane_restr / Dev ideal: 0.01

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