[English] 日本語
Yorodumi- PDB-5fyo: Calcium-dependent phosphoinositol-specific phospholipase C from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fyo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 1 | |||||||||
Components | PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C | |||||||||
Keywords | HYDROLASE / PI-PLC / GRAM-NEGATIVE / CALCIUM-DEPENDENT / HYDROLASE APO FORM | |||||||||
Function / homology | Phosphoinositide phospholipase C, Ca2+-dependent / Phosphoinositide phospholipase C, Ca2+-dependent / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Phosphoinositol-specific phospholipase c Function and homology information | |||||||||
Biological species | PSEUDOMONAS SP. (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Norgaard, A. / Segura, D.R. / Blicher, T.H. / Wilson, K.S. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2017 Title: The structure of a calcium-dependent phosphoinositide-specific phospholipase C from Pseudomonas sp. 62186, the first from a Gram-negative bacterium. Authors: Moroz, O.V. / Blagova, E. / Lebedev, A.A. / Nrgaard, A. / Segura, D.R. / Blicher, T.H. / Brask, J. / Wilson, K.S. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fyo.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fyo.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 5fyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fyo_validation.pdf.gz | 441.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fyo_full_validation.pdf.gz | 442.7 KB | Display | |
Data in XML | 5fyo_validation.xml.gz | 27.5 KB | Display | |
Data in CIF | 5fyo_validation.cif.gz | 40.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fyo ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fyo | HTTPS FTP |
-Related structure data
Related structure data | 5fypC 5fyrC 3h4wS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 32775.258 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS SP. (bacteria) / Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: A0A1S4NYD4*PLUS #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % / Description: NONE |
---|---|
Crystal grow | Method: vapor diffusion, hanging drop / pH: 10 Details: PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.81 Å / Num. obs: 85192 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3H4W Resolution: 1.5→48.81 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU B: 2.592 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES B87-B90 ARE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.65 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→48.81 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|