[English] 日本語
Yorodumi- PDB-3d1o: Structure of the PTP-Like Phytase Expressed by Selenomonas Rumina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d1o | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the PTP-Like Phytase Expressed by Selenomonas Ruminantium at an Ionic Strength of 300 mM | ||||||
Components | Myo-inositol hexaphosphate phosphohydrolase | ||||||
Keywords | HYDROLASE / PTP / PROTEIN TYROSINE PHOSPHATASE / PHYTASE / P-LOOP / IONIC STRENGTH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Selenomonas ruminantium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Gruninger, R.J. / Selinger, L.B. / Mosimann, S.C. | ||||||
Citation | Journal: Febs J. / Year: 2008 Title: Effect of ionic strength and oxidation on the P-loop conformation of the protein tyrosine phosphatase-like phytase, PhyAsr. Authors: Gruninger, R.J. / Brent Selinger, L. / Mosimann, S.C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3d1o.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3d1o.ent.gz | 116.1 KB | Display | PDB format |
PDBx/mmJSON format | 3d1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/3d1o ftp://data.pdbj.org/pub/pdb/validation_reports/d1/3d1o | HTTPS FTP |
---|
-Related structure data
Related structure data | 2pszC 2pt0C 3d1hC 3d1qC 2b4pS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38987.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Selenomonas ruminantium (bacteria) / Gene: phyA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7WUJ1 #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.76 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 10% P8K, 250 MM NACL, 50 MM NA-ACETATE, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 20, 2006 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 53330 / Num. obs: 52151 / % possible obs: 91.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.047 / Χ2: 1.043 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3 / Num. unique all: 3342 / Rsym value: 0.249 / Χ2: 1.073 / % possible all: 50.6 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2b4p Resolution: 2.1→50 Å / FOM work R set: 0.869 / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||
Solvent computation | Bsol: 46.322 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.453 Å2
| ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
| ||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||
Xplor file |
|