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Yorodumi- PDB-4wn3: Crystal structure of Saccharomyces cerevisiae OMP synthase in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wn3 | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(NH)P | ||||||
Components | Orotate phosphoribosyltransferase 1 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information pyrimidine ribonucleoside biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleotide biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bang, M.B. / Molich, U. / Hansen, M.R. / Grubmeyer, C. / Harris, P. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Saccharomyces cerevisiae OMP synthase in complex with PRP(NH)P Authors: Bang, M.B. / Molich, U. / Hansen, M.R. / Grubmeyer, C. / Harris, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wn3.cif.gz | 61.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wn3.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 4wn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wn3_validation.pdf.gz | 787.5 KB | Display | wwPDB validaton report |
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Full document | 4wn3_full_validation.pdf.gz | 792 KB | Display | |
Data in XML | 4wn3_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4wn3_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/4wn3 ftp://data.pdbj.org/pub/pdb/validation_reports/wn/4wn3 | HTTPS FTP |
-Related structure data
Related structure data | 4wmlS S: Starting model for refinement |
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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: 25484.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: URA5, PYR5, YML106W, YM8339.13 / Production host: Escherichia coli (E. coli) References: UniProt: P13298, orotate phosphoribosyltransferase |
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#2: Chemical | ChemComp-MG / |
#3: Sugar | ChemComp-3R3 / [[[( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Na HEPES pH 7.5, 10 % isopropanol, 20 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→33.14 Å / Num. obs: 24622 / % possible obs: 99.3 % / Redundancy: 14.2 % / Rsym value: 0.06 / Net I/σ(I): 28.36 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 1.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WML Resolution: 1.8→29.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.732 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.653 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→29.17 Å
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Refine LS restraints |
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