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Yorodumi- PDB-3pnu: 2.4 Angstrom Crystal Structure of Dihydroorotase (pyrC) from Camp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pnu | ||||||
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Title | 2.4 Angstrom Crystal Structure of Dihydroorotase (pyrC) from Campylobacter jejuni. | ||||||
Components | Dihydroorotase | ||||||
Keywords | HYDROLASE / TIM barrel / Dihydroorotase / Zinc binding / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information dihydroorotase / pyrimidine nucleobase biosynthetic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Campylobacter jejuni subsp. jejuni (Campylobacter) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: 2.4 Angstrom Crystal Structure of Dihydroorotase (pyrC) from Campylobacter jejuni. Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pnu.cif.gz | 155.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pnu.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3pnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/3pnu ftp://data.pdbj.org/pub/pdb/validation_reports/pn/3pnu | HTTPS FTP |
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-Related structure data
Related structure data | 1j79S S: Starting model for refinement |
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Similar structure data | |
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: 41263.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter) Strain: NCTC 11168 / Gene: Cj0259, pyrC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q0PBP6, dihydroorotase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 7.7 mg/mL, 0.25M Sodium cloride, Tris-HCl (pH 8.3); Screen: PACT (F9), 0.2M Potassium/Sodium tartrate, 0.1M Bis TRIS propane (pH 6.5), 20% w/v PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2010 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 35063 / Num. obs: 35063 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 51.2 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 25 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1709 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J79 Resolution: 2.4→29.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.429 / SU ML: 0.174 Isotropic thermal model: Thermal factors individually refined Cross valid method: THROUGHOUT / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.677 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→29.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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