+Open data
-Basic information
Entry | Database: PDB / ID: 1yoo | ||||||
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Title | ASPARTATE AMINOTRANSFERASE MUTANT ATB17 WITH ISOVALERIC ACID | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | 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 | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Oue, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yoo.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yoo.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yoo_validation.pdf.gz | 398.5 KB | Display | wwPDB validaton report |
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Full document | 1yoo_full_validation.pdf.gz | 404.6 KB | Display | |
Data in XML | 1yoo_validation.xml.gz | 9.8 KB | Display | |
Data in CIF | 1yoo_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/1yoo ftp://data.pdbj.org/pub/pdb/validation_reports/yo/1yoo | HTTPS FTP |
-Related structure data
Related structure data | 1artS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-IVA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE ...THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANS |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 8, 1998 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 24.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Rfactor obs: 0.199 |