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- PDB-1yoo: ASPARTATE AMINOTRANSFERASE MUTANT ATB17 WITH ISOVALERIC ACID -

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Basic information

Entry
Database: PDB / ID: 1yoo
TitleASPARTATE AMINOTRANSFERASE MUTANT ATB17 WITH ISOVALERIC ACID
ComponentsASPARTATE AMINOTRANSFERASEAspartate transaminase
KeywordsAMINOTRANSFERASE
Function / homology
Function and homology information


L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic 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
ISOVALERIC ACID / PYRIDOXAL-5'-PHOSPHATE / Aspartate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOue, S. / Okamoto, A. / Yano, T. / Kagamiyama, H.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues.
Authors: Oue, S. / Okamoto, A. / Yano, T. / Kagamiyama, H.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Directed Evolution of an Aspartate Aminotransferase with New Substrate Specificities
Authors: Yano, T. / Oue, S. / Kagamiyama, H.
History
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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)43,9683
Polymers43,6191
Non-polymers3492
Water2,414134
1
A: ASPARTATE AMINOTRANSFERASE
hetero molecules

A: ASPARTATE AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9376
Polymers87,2382
Non-polymers6994
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area7630 Å2
ΔGint-34 kcal/mol
Surface area28920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.000, 84.840, 78.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ASPARTATE AMINOTRANSFERASE / Aspartate transaminase / ASPAT


Mass: 43619.184 Da / Num. of mol.: 1
Mutation: A11T, F24L, N34D, I37M, K41N, K126R, S139G, N142T, A269T, A293V, N297S, S311G, I353T, S361F, S363G, V387L, M397L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: 293 / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): TY103 / References: UniProt: P00509, aspartate transaminase
#2: 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
#3: Chemical ChemComp-IVA / ISOVALERIC ACID / 3-Methylbutanoic acid


Mass: 102.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE ...THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE TRADITIONALLY USED IN ALL PUBLICATIONS CONCERNING ASPARTATE AMINOTRANSFERASES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
20.2 Msodium isovalerate1drop
31.6 Mammonium sulfate1reservoir
40.1 MNa-HEPES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 8, 1998 / Details: MIRROR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→75 Å / Num. obs: 17348 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.0563 / Net I/σ(I): 19.8
Reflection shellResolution: 2.4→2.8 Å / Redundancy: 2 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 3.2 / % possible all: 98.3
Reflection
*PLUS
Num. measured all: 61169 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 98.3 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
PROCESS(RIGAKU)data reduction
PROCESS(RIGAKU)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ART

1art


Resolution: 2.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1591 9.9 %RANDOM
Rwork0.162 ---
obs0.162 16005 77.7 %-
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3069 0 22 134 3225
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.081.5
X-RAY DIFFRACTIONx_mcangle_it1.832
X-RAY DIFFRACTIONx_scbond_it1.962
X-RAY DIFFRACTIONx_scangle_it3.212.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 225 10 %
Rwork0.199 2025 -
obs--66.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.27
LS refinement shell
*PLUS
Rfactor obs: 0.199

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