[English] 日本語
Yorodumi- PDB-3mjd: 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransfera... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mjd | ||||||
---|---|---|---|---|---|---|---|
Title | 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella tularensis. | ||||||
Components | Orotate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Orotate / Phosphoribosyltransferase / idp02311 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases | ||||||
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 | Francisella tularensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Minasov, G. / 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: 1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella tularensis. Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3mjd.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3mjd.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 3mjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mjd_validation.pdf.gz | 482 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3mjd_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 3mjd_validation.xml.gz | 37.9 KB | Display | |
Data in CIF | 3mjd_validation.cif.gz | 56 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mjd ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mjd | HTTPS FTP |
-Related structure data
Related structure data | 1oroS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | Chains A and B, C and D form two biological dimers. |
-Components
#1: Protein | Mass: 26114.830 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella tularensis (bacteria) / Strain: SCHU S4 / Gene: FTT0437c, FTT_0437c, pyrE / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 References: UniProt: Q5NHL5, orotate phosphoribosyltransferase #2: Chemical | ChemComp-EDO / | #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.57 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution: 7.5 mg/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: Classics II G1, 0.2M Sodium chloride, 0.1M TRIS (pH 8.5), 25% PEG 3350., VAPOR DIFFUSION, ...Details: Protein solution: 7.5 mg/mL, 0.25M Sodium Chloride, 0.01M Tris-HCL (pH 8.3); Screen solution: Classics II G1, 0.2M Sodium chloride, 0.1M TRIS (pH 8.5), 25% PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 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: 1.9→30 Å / Num. all: 71519 / Num. obs: 71519 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3530 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ORO Resolution: 1.9→29.47 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.323 / SU ML: 0.099 / Isotropic thermal model: Refined Individually / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.671 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→29.47 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|