+Open data
-Basic information
Entry | Database: PDB / ID: 2d5y | ||||||
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Title | Aspartate Aminotransferase Mutant MC With Isovaleric Acid | ||||||
Components | Aspartate aminotransferase | ||||||
Keywords | TRANSFERASE / aspartate aminotransferase / directed evolution / protein design / protein enginnering | ||||||
Function / homology | Function and homology information L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 Å | ||||||
Authors | Tanaka, Y. / Nakagawa, N. / Tada, H. / Yano, T. / Masui, R. / Kuramitsu, S. | ||||||
Citation | Journal: To be Published Title: The Structures of Aspartate Aminotransferase with Mutations of Non-Active-Site Residues Authors: Tanaka, Y. / Nakagawa, N. / Tada, H. / Yano, T. / Masui, R. / Kuramitsu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2d5y.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2d5y.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 2d5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2d5y_validation.pdf.gz | 460.6 KB | Display | wwPDB validaton report |
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Full document | 2d5y_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 2d5y_validation.xml.gz | 18.2 KB | Display | |
Data in CIF | 2d5y_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/2d5y ftp://data.pdbj.org/pub/pdb/validation_reports/d5/2d5y | HTTPS FTP |
-Related structure data
Related structure data | 2d61C 2d63C 2d64C 2d65C 2d66C 2d7yC 2d7zC C: citing same article (ref.) |
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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: 43664.266 Da / Num. of mol.: 1 Mutation: A11T, A293V, N297S, I353T, S361F, S363G, V387L, M397L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Gene: aspC / 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 35% Na2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 1, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. all: 36941 / Num. obs: 36941 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.1 Å2 |
Reflection shell | Resolution: 1.98→2.05 Å / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→37.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 295789.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.9821 Å2 / ksol: 0.333983 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→37.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.98→2.1 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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