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- PDB-3aat: ACTIVITY AND STRUCTURE OF THE ACTIVE-SITE MUTANTS R386Y AND R386F... -

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Basic information

Entry
Database: PDB / ID: 3aat
TitleACTIVITY AND STRUCTURE OF THE ACTIVE-SITE MUTANTS R386Y AND R386F OF ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE(AMINOTRANSFERASE)
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
PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsDanishefsky, A.T. / Ringe, D. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Activity and structure of the active-site mutants R386Y and R386F of Escherichia coli aspartate aminotransferase.
Authors: Danishefsky, A.T. / Onnufer, J.J. / Petsko, G.A. / Ringe, D.
#1: Journal: Biochemistry / Year: 1989
Title: 2.8-Angstroms-Resolution Crystal Structure of an Active-Site Mutant of Aspartate Aminotransferse from Escherichia Coli
Authors: Smith, D.L. / Almo, S.C. / Toney, M.D. / Ringe, D.
#2: Journal: J.Mol.Biol. / Year: 1986
Title: Preliminary X-Ray Data for Aspartate Aminotransferase from Escherichia Coli
Authors: Smith, D.L. / Ringe, D. / Finlayson, W.L. / Kirsch, J.F.
History
DepositionDec 6, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Structure summary
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9523
Polymers43,6091
Non-polymers3432
Water00
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9056
Polymers87,2182
Non-polymers6864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7940 Å2
ΔGint-68 kcal/mol
Surface area28920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.000, 87.600, 78.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES 138 AND 195 ARE CIS PROLINES.
DetailsTHE MOLECULE IS A DIMER. TO GENERATE THE OTHER CHAIN ONE MUST APPLY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, 87.60-Y, 78.80-Z) TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43609.191 Da / Num. of mol.: 1 / Mutation: R374F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
Sequence detailsTHE RESIDUE NUMBERING USED IN THIS ENTRY HAS BEEN CHOSEN TO MAXIMIZE HOMOLOGY WITH OTHER SPECIES OF ...THE RESIDUE NUMBERING USED IN THIS ENTRY HAS BEEN CHOSEN TO MAXIMIZE HOMOLOGY WITH OTHER SPECIES OF THE ENZYME. THEREFORE, THE RESIDUE NUMBERING STARTS WITH 5 AND RESIDUE NUMBERS 128 - 132, 153, 232, AND 407 HAVE NOT BEEN USED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.14 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 %satammonium sulfate1reservoir
220 mMpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.067

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→10 Å / Rfactor obs: 0.215
Details: THE GEOMETRY AT MANY OF THE COIL REGIONS WAS NOT CLEARLY DEFINED IN THE ELECTRON DENSITY MAPS.
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 20 0 3088
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0730.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0750.07
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 10531 / σ(I): 1 / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12 Å2

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