+Open data
-Basic information
Entry | Database: PDB / ID: 2yzj | ||||||
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Title | Crystal structure of dCTP deaminase from Sulfolobus tokodaii | ||||||
Components | 167aa long hypothetical dUTPase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / All beta proteins / Hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information dCTP deaminase activity / nucleobase-containing small molecule interconversion / dUTP diphosphatase / dUTP diphosphatase activity Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å | ||||||
Authors | Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of dCTP deaminase from Sulfolobus tokodaii Authors: Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yzj.cif.gz | 110.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yzj.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yzj_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2yzj_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2yzj_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2yzj_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yz/2yzj ftp://data.pdbj.org/pub/pdb/validation_reports/yz/2yzj | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19190.639 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q970G0, UniProt: F9VNI5*PLUS #2: Chemical | #3: Chemical | ChemComp-TRS / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.17M Magnesium Acetate, 0.085M Sodium Cavpdylate pH 6.5, 17% PEG 8000, 0.01M dUTP, 0.01M Magnesium Chloride, 0.02M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9794, 0.9000 | ||||||||||||
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 9, 2006 | ||||||||||||
Radiation | Monochromator: Fixed exit Si double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→50 Å / Num. obs: 90293 / % possible obs: 92 % / Redundancy: 2.7 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.121 | ||||||||||||
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.236 / Num. unique all: 2304 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.66→31.65 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 131238.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.0355 Å2 / ksol: 0.35681 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.66→31.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.63 Å / Total num. of bins used: 6 /
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Xplor file |
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