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- PDB-1ahe: ASPARTATE AMINOTRANSFERASE HEXAMUTANT -

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Basic information

Entry
Database: PDB / ID: 1ahe
TitleASPARTATE AMINOTRANSFERASE HEXAMUTANT
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsTRANSFERASE (AMINOTRANSFERASE)
Function / homology
Function and homology information


L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / cytosol / cytoplasm
Aspartate/other aminotransferase / Aminotransferase, class I/classII / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase / Pyridoxal phosphate-dependent transferase domain 1 / Pyridoxal phosphate-dependent transferase, major domain / Aminotransferases, class-I, pyridoxal-phosphate-binding site
Aspartate aminotransferase
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 22, 1995-
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,9616
Polymers87,2752
Non-polymers6864
Water7,206400
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-70 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)85.070, 77.980, 88.860
Angle α, β, γ (deg.)90.00, 118.63, 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, 0.00046, 0.0001), (-0.00046, -1, -0.0002), (0.0001, -0.0002, 1)
Vector: -0.03099, 83.29076, 0.00206)
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 0.188

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Components

#1: Protein/peptide ASPARTATE AMINOTRANSFERASE / Aspartate transaminase / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Pyridoxal phosphate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O / Water
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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-ID
114 mg/mlproteindrop
220 mMpotassium phosphatedrop
30.01 mMPLPdrop
42 mMEDTAdrop
50.5 mMDTTdrop
61.90-1.95 Mammonium sulfatereservoir
7200 mMN-methylmorpholinereservoir
82 %PEG400reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorDetector: AREA DETECTOR / Date: Sep 14, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 1.9 % / Biso Wilson estimate: 41.2 Å2
Reflection
*PLUS
Num. obs: 42704 / % possible obs: 88.6 % / Observed criterion σ(I): 1

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Processing

Software
NameClassification
TNTrefinement
MADNESdata reduction
RefinementResolution: 2.3→8 Å / σ(F): 1 /
RfactorNum. reflection% reflection
Obs0.203 42358 96 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6142 0 40 400 6582
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumberWeight
t_bond_d0.01363060.02
t_angle_deg2.2785203
t_dihedral_angle_d24.9374615
t_incorr_chiral_ct0
t_pseud_angle
t_trig_c_planes0.0051700.02
t_gen_planes0.0119220.02
t_it3.5166000.2
t_nbd0.0241600.1

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