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Yorodumi- PDB-5fyr: Calcium-dependent phosphoinositol-specific phospholipase C from a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fyr | ||||||
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Title | Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, myoinositol complex | ||||||
Components | PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C | ||||||
Keywords | HYDROLASE / PI-PLC / BACTERIAL / PSEUDOMONAS / GRAM-NEGATIVE / CALCIUM-DEPENDENT / MYOINOSITOL COMPLEX | ||||||
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 / 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE / PHOSPHATE ION / Phosphoinositol-specific phospholipase c Function and homology information | ||||||
Biological species | PSEUDOMONAS SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fyr.cif.gz | 502.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fyr.ent.gz | 414.4 KB | Display | PDB format |
PDBx/mmJSON format | 5fyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fyr ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fyr | HTTPS FTP |
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-Related structure data
Related structure data | 5fyoC 5fypSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 32775.258 Da / Num. of mol.: 4 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 | ChemComp-INS / #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.4 % / Description: NONE |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→48.93 Å / Num. obs: 184175 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FYP Resolution: 1.45→48.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.343 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 16.818 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→48.93 Å
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Refine LS restraints |
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