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- PDB-1asf: THE STRUCTURAL BASIS FOR THE REDUCED ACTIVITY OF THE Y226F(Y225F)... -

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Basic information

Entry
Database: PDB / ID: 1asf
TitleTHE STRUCTURAL BASIS FOR THE REDUCED ACTIVITY OF THE Y226F(Y225F) ACTIVE SITE MUTANT OF E. COLI ASPARTATE AMINOTRANSFERASE
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsAMINOTRANSFERASE
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 / 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
AuthorsSchumacher, C. / Ringe, D.
Citation
Journal: To be Published
Title: The Structural Basis for the Reduced Activity of the Y226F(Y225F) Active Site Mutant of E. Coli Aspartate Aminotransferase
Authors: Schumacher, C. / Ringe, D.
#1: 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.
#2: Journal: Biochemistry / Year: 1989
Title: 2.8 Angstroms 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.
History
DepositionAug 27, 1993-
Revision 1.0Apr 30, 1994Provider: 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

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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)43,9463
Polymers43,6031
Non-polymers3432
Water0
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8936
Polymers87,2062
Non-polymers6864
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7810 Å2
ΔGint-67 kcal/mol
Surface area29910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)156.800, 87.300, 80.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: ALA 20 - PRO 21 OMEGA =301.68 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
2: ASP 23 - PRO 24 OMEGA =219.63 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: ARG 37 - PRO 38 OMEGA = 34.79 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
4: CIS PROLINE - PRO 140 / 5: CIS PROLINE - PRO 196
6: ASP 200 - PRO 201 OMEGA =147.72 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsTHE MOLECULE IS A DIMER. TO GENERATE THE OTHER CHAIN ONE MUST APPLY THE CRYSTALLOGRAPHIC SYMMETRY OPERATION (X, 87.3-Y, 80.19-Z) TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / Aspartate transaminase


Mass: 43603.211 Da / Num. of mol.: 1 / Mutation: Y214F
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 / Sulfate


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


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
Nonpolymer detailsHET GROUP PLP 258 IS BOUND TO LYS 258 FORMING A PROTONATED SCHIFF BASE LINKAGE (BETWEEN NZ LYS 258 ...HET GROUP PLP 258 IS BOUND TO LYS 258 FORMING A PROTONATED SCHIFF BASE LINKAGE (BETWEEN NZ LYS 258 AND C4A PLP 258).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.9 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.22 / Rfactor obs: 0.22 / Highest resolution: 2.8 Å
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3068 0 20 0 3088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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