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Yorodumi- PDB-1uf4: Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino aci... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uf4 | ||||||
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Title | Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid amidohydrolase | ||||||
Components | N-carbamyl-D-amino acid amidohydrolase | ||||||
Keywords | HYDROLASE / N-carbamyl-D-amino acid amidohydrolase / D-amino acid | ||||||
Function / homology | Function and homology information N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity / : Similarity search - Function | ||||||
Biological species | Agrobacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Hashimoto, H. / Aoki, M. / Shimizu, T. / Nakai, T. / Morikawa, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. | ||||||
Citation | Journal: To be published Title: Crystal structure of C171A/V236A Mutant of N-carbamyl-D-amino acid Authors: Hashimoto, H. / Aoki, M. / Shimizu, T. / Nakai, T. / Morikawa, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uf4.cif.gz | 136.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uf4.ent.gz | 107.7 KB | Display | PDB format |
PDBx/mmJSON format | 1uf4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/1uf4 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/1uf4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 34138.977 Da / Num. of mol.: 2 / Mutation: C171A/V236A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium sp. (bacteria) / Plasmid: pAD108 / Production host: Escherichia coli (E. coli) References: UniProt: P60327, N-carbamoyl-D-amino-acid hydrolase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 41.77 % |
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→68.43 Å / Num. obs: 34273 / Biso Wilson estimate: 22.7 Å2 |
-Processing
Software | Name: CNS / Version: 1.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→68.42 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1873417.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.3958 Å2 / ksol: 0.361501 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→68.42 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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