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- PDB-1qir: ASPARTATE AMINOTRANSFERASE FROM ESCHERICHIA COLI, C191Y MUTATION,... -

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Basic information

Entry
Database: PDB / ID: 1qir
TitleASPARTATE AMINOTRANSFERASE FROM ESCHERICHIA COLI, C191Y MUTATION, WITH BOUND MALEATE
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsAMINOTRANSFERASE / TRANSFERASE(AMINOTRANSFERASE) / PYRIDOXAL PHOSPHATE / MALEATE
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
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
MALEIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJeffery, C.J. / Gloss, L.M. / Petsko, G.A. / Ringe, D.
CitationJournal: Protein Eng. / Year: 2000
Title: The Role of Residues Outside the Active Site in Catalysis: Structural Basis for Function of C191 Mutants of E. Coli Aspartate Aminotransferase
Authors: Jeffery, C.J. / Gloss, L.M. / Petsko, G.A. / Ringe, D.
History
DepositionJun 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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)44,0423
Polymers43,6791
Non-polymers3632
Water1,42379
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0856
Polymers87,3582
Non-polymers7264
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7710 Å2
ΔGint-39 kcal/mol
Surface area34580 Å2
MethodPQS
Unit cell
Length a, b, c (Å)157.180, 85.400, 78.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsBIOLOGICAL_UNIT: ACTIVE AS A DIMER

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43679.246 Da / Num. of mol.: 1 / Fragment: COMPLETE SUBUNIT / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL PHOSPHATE COFACTOR COVALENTLY BOUND TO LYS258 VIA SCHIFF BASE LINKAGE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: CYTOPLASM / Cellular location (production host): CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsNUMBERED TO MATCH NUMBERING OF CHICKEN CYTOPLASMIC ASPARTATE AMINOTRANSFERASE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 %
Crystal growpH: 7.5
Details: PROTEIN SOLUTION: 6MG/ML PROTEIN, 20 MM POTASSIUM PHOSPHATE BUFFER, PH 7.5, 10 UM PLP, 5 MM EDTA, RESERVOIR SOLUTION: 20MM POTASSIUM PHOSPHATE BUFFER, PH 7.5, AND 45-50% AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
220 mMpotassium phosphate1drop
30.01 mMPLP1drop
45 mMEDTA1drop
540-54 %ammonium sulfate1reservoir
620 mMpotassium phosphate1reservoir
75 mMinhibitor maleate1drop

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34520 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Rmerge(I) obs: 0.06
Reflection shellHighest resolution: 2.2 Å

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
R-AXISdata reduction
R-AXISdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ASA

1asa


Resolution: 2.2→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.185 --
obs0.185 34520 80 %
Displacement parametersBiso mean: 25.09 Å2
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 23 79 3177
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.064
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.949
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.502
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.94
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.502

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