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- PDB-1ahf: ASPARTATE AMINOTRANSFERASE HEXAMUTANT -

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Basic information

Entry
Database: PDB / ID: 1ahf
TitleASPARTATE AMINOTRANSFERASE HEXAMUTANT
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
INDOLYLPROPIONIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsMalashkevich, V.N. / Jansonius, J.N.
Citation
Journal: Nat.Struct.Biol. / Year: 1995
Title: Alternating arginine-modulated substrate specificity in an engineered tyrosine aminotransferase.
Authors: Malashkevich, V.N. / Onuffer, J.J. / Kirsch, J.F. / Jansonius, J.N.
#1: Journal: Biochemistry of Vitamin B6 and Pqq / Year: 1994
Title: Redesign of Aspartate Aminotransferase Specificity to that of Tyrosine Aminotransferase
Authors: Kirsch, J.F. / Onuffer, J.J.
History
DepositionFeb 22, 1995Processing site: BNL
Revision 1.0Sep 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 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

Downloads & links

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Assembly

Deposited unit
A: ASPARTATE AMINOTRANSFERASE
B: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,0546
Polymers87,2752
Non-polymers7804
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8310 Å2
ΔGint-43 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.920, 79.390, 88.800
Angle α, β, γ (deg.)90.00, 118.99, 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: (-1, 0.00091, 0.00038), (-0.00091, -1, -0.00059), (0.00038, -0.00059, 1)
Vector: 0.00667, 83.30071, 0.01655)
DetailsMTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 409 B 5 .. B 409 0.236

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / ASPARTATE TRANSAMINASE


Mass: 43637.293 Da / Num. of mol.: 2 / Mutation: V39L, K41Y, T47I, N69L, T109S, N297S
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-IOP / INDOLYLPROPIONIC ACID


Mass: 189.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND SUBSTRATE SPECIFICITY CHANGED TO THAT OF TYROSINE AMINOTRANSFERASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
220 mMpotassium phosphate1drop
30.01 mMPLP1drop
42 mMEDTA1drop
50.5 mMDTT1drop
61.90-1.95 Mammonium sulfate1reservoir
7200 mMN-methylmorpholine1reservoir
82 %PEG4001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 1.2 % / Biso Wilson estimate: 44.6 Å2
Reflection
*PLUS
Num. obs: 46105 / % possible obs: 97.3 % / Observed criterion σ(I): 1

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Processing

Software
NameClassification
TNTrefinement
XDSdata reduction
RefinementResolution: 2.3→8 Å / σ(F): 1 /
RfactorNum. reflection% reflection
obs0.232 46004 99 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 49 402 6593
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01363170.02
X-RAY DIFFRACTIONt_angle_deg2.385343
X-RAY DIFFRACTIONt_dihedral_angle_d25.4374915
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0051710.02
X-RAY DIFFRACTIONt_gen_planes0.0129230.02
X-RAY DIFFRACTIONt_it3.5466040.2
X-RAY DIFFRACTIONt_nbd0.0172450.1

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