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Yorodumi- PDB-4ohc: Crystal structure of orotate phosphoribosyltransferase (OPRTase) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ohc | ||||||
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Title | Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia | ||||||
Components | Orotate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / OPRT / OPRTase | ||||||
Function / homology | Function and homology information orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / nucleoside metabolic process / 'de novo' UMP biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of orotate phosphoribosyltransferase (OPRTase) from Burkholderia cenocepacia Authors: Lukacs, C.M. / Abendroth, J. / 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 | 4ohc.cif.gz | 541.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ohc.ent.gz | 447.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ohc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ohc_validation.pdf.gz | 495.9 KB | Display | wwPDB validaton report |
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Full document | 4ohc_full_validation.pdf.gz | 502.3 KB | Display | |
Data in XML | 4ohc_validation.xml.gz | 60 KB | Display | |
Data in CIF | 4ohc_validation.cif.gz | 88.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oh/4ohc ftp://data.pdbj.org/pub/pdb/validation_reports/oh/4ohc | HTTPS FTP |
-Related structure data
Related structure data | 3m3hS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 26561.299 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: pyrE, BCAL0204 / Production host: Escherichia coli (E. coli) References: UniProt: B4E589, orotate phosphoribosyltransferase #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-NA / #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: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: JCSG+ g6: 200mM sodium malonate, 20% PEG 3350, 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: 0.97872 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 11, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Highest resolution: 1.85 Å / Num. all: 134209 / Num. obs: 130679 / % possible obs: 97.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.06 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 2.75 / Num. unique all: 9459 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3m3h Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.188 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / 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: 25.629 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→50 Å
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