[English] 日本語
Yorodumi- PDB-3qvq: The structure of an Oleispira antarctica phosphodiesterase OLEI02... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qvq | ||||||
---|---|---|---|---|---|---|---|
Title | The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate | ||||||
Components | Phosphodiesterase Olei02445 | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta hydrolase | ||||||
Function / homology | Phosphatidylinositol (PI) phosphodiesterase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / SN-GLYCEROL-3-PHOSPHATE / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER Function and homology information | ||||||
Biological species | Oleispira antarctica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.602 Å | ||||||
Authors | Singer, A.U. / Kagan, O. / Evdokimova, E. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of an Oleispira antarctica phosphodiesterase OLEI02445 in complex with the product sn-glycerol-3-phosphate Authors: Singer, A.U. / Kagan, O. / Evdokimova, E. / Cuff, M.E. / Edwards, A.M. / Joachimiak, A. / Yakunin, A.F. / Savchenko, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3qvq.cif.gz | 231.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3qvq.ent.gz | 193.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3qvq_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3qvq_full_validation.pdf.gz | 493.2 KB | Display | |
Data in XML | 3qvq_validation.xml.gz | 47.2 KB | Display | |
Data in CIF | 3qvq_validation.cif.gz | 69.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/3qvq ftp://data.pdbj.org/pub/pdb/validation_reports/qv/3qvq | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28043.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: TEV cleaved / Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: OLEI02445 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: glycerophosphocholine phosphodiesterase |
---|
-Non-polymers , 8 types, 968 molecules
#2: Chemical | ChemComp-G3P / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-NI / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.22 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2M Magnesium Chloride, 0.1M Bis-Tris pH6.5, 25% PEG3350, cocrystallized with 2.5mM Glycero-3Phosphocholine, and cryoprotected with Paratone-N oil, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97937 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 28, 2009 / Details: Mirrors |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97937 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→37.259 Å / Num. all: 123770 / Num. obs: 122939 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 31.893 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5694 / Rsym value: 0.374 / % possible all: 93.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD Starting model: none Resolution: 1.602→37.259 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 19.25 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.945 Å2 / ksol: 0.391 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.602→37.259 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION
|