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Yorodumi- PDB-4lfy: Crystal structure of a dihydroorotase from Burkholderia cenocepac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lfy | ||||||
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Title | Crystal structure of a dihydroorotase from Burkholderia cenocepacia J2315 | ||||||
Components | Dihydroorotase | ||||||
Keywords | HYDROLASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / carboxylated lysine | ||||||
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 | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a dihydroorotase from Burkholderia cenocepacia J2315 Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lfy.cif.gz | 285.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lfy.ent.gz | 228.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lfy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lf/4lfy ftp://data.pdbj.org/pub/pdb/validation_reports/lf/4lfy | 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 40862.484 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: pyrC, BceJ2315_32910, BCAL3351 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EEU0, dihydroorotase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CA / #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: 2.26 Å3/Da / Density % sol: 45.46 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.4 Details: 0.1M Tris HCl, 18% PEG4000, 0.2M CaCl2, pH 8.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-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 225 mm CCD / Detector: CCD / Date: Jun 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 69475 / Num. obs: 69409 / % possible obs: 99.9 % / Redundancy: 6.16 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 6.17 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 3.85 / Num. unique all: 5049 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1j79 Resolution: 1.8→46 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.881 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.104 / 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: 19.448 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→46 Å
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Refine LS restraints |
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