[English] 日本語
Yorodumi- PDB-3m3h: 1.75 Angstrom resolution crystal structure of an orotate phosphor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m3h | ||||||
---|---|---|---|---|---|---|---|
Title | 1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' | ||||||
Components | Orotate phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Orotate Phosphoribosyltransferase / Pyrimidine Ribonucleotide Biosynthesis / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Glycosyltransferase / Magnesium / Pyrimidine biosynthesis | ||||||
Function / homology | Function and homology information orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / 'de novo' UMP biosynthetic process / magnesium ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor' Authors: Halavaty, A.S. / Shuvalova, L. / Minasov, G. / Winsor, J. / Dubrovska, I. / Kwon, K. / 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 | 3m3h.cif.gz | 58.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3m3h.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 3m3h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m3h_validation.pdf.gz | 430.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3m3h_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 3m3h_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 3m3h_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3h ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3h | HTTPS FTP |
-Related structure data
Related structure data | 3dezS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 25484.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: 'Ames Ancestor' / Gene: pyrE, BA_4021, GBAA_4021, BAS3733 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus References: UniProt: Q81WF6, orotate phosphoribosyltransferase | ||
---|---|---|---|
#2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.5 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 7.7 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Classic II condition (CS2) A8 (#8). Cryo condition 2.5 M KCl and 25% sucrose. 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 4, 2010 / Details: Be Lenses/Diamond Laue Mono |
Radiation | Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. all: 19414 / Num. obs: 19414 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 13.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 5.7 / Num. unique all: 960 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DEZ Resolution: 1.75→28.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.713 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 19.589 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→28.43 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.751→1.796 Å / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|