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- PDB-2aat: 2.8-ANGSTROMS-RESOLUTION CRYSTAL STRUCTURE OF AN ACTIVE-SITE MUTA... -

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Basic information

Entry
Database: PDB / ID: 2aat
Title2.8-ANGSTROMS-RESOLUTION CRYSTAL STRUCTURE OF AN ACTIVE-SITE MUTANT OF ASPARTATE AMINOTRANSFERASE FROM ESCHERICHIA COLI
ComponentsASPARTATE AMINOTRANSFERASE
KeywordsTRANSFERASE(AMINOTRANSFERASE)
Function / homology
Function and homology information


L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol
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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsSmith, D. / Almo, S.C. / Toney, M. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1989
Title: 2.8-A-resolution crystal structure of an active-site mutant of aspartate aminotransferase from Escherichia coli.
Authors: Smith, D.L. / Almo, S.C. / Toney, M.D. / Ringe, D.
#1: 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
DepositionMay 30, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 25, 2012Group: Structure summary
Revision 1.4Jul 29, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / pdbx_database_status ...audit_author / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _audit_author.name / _pdbx_database_status.process_site ..._audit_author.name / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)43,9053
Polymers43,5611
Non-polymers3442
Water00
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8116
Polymers87,1222
Non-polymers6884
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area8080 Å2
ΔGint-60 kcal/mol
Surface area31150 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.800, 86.740, 79.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES 140 AND 196 ARE CIS PROLINES.
DetailsTHE MOLECULE IS A DIMER. TO GENERATE THE OTHER CHAIN ONE MUST APPLY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, 86.74-Y, 79.84-Z) TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE


Mass: 43561.109 Da / Num. of mol.: 1 / Mutation: K246A
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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
Sequence detailsTHE RESIDUE NUMBERING USED IN THIS ENTRY HAS BEEN CHOSEN TO MAXIMIZE HOMOLOGY BETWEEN E. COLI ...THE RESIDUE NUMBERING USED IN THIS ENTRY HAS BEEN CHOSEN TO MAXIMIZE HOMOLOGY BETWEEN E. COLI AATASE AND CHICKEN MITOCHONDRIAL AATASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.51 %
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.2 mg/mLprotein solution11
250 mMpotassium phosphate11
353 %satammonium sulfate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 8783 / % possible obs: 64 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→10 Å /
RfactorNum. reflection
obs0.22 8433
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 21 0 3086
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0710.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0640.07
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: 2.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 8433 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 14 Å2

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