[English] 日本語
Yorodumi- PDB-5d91: Structure of a phosphatidylinositolphosphate (PIP) synthase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d91 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum | ||||||
Components | AF2299 protein,Phosphatidylinositol synthase | ||||||
Keywords | MEMBRANE PROTEIN / Enzyme / lipid biosynthesis / phosphatidylinositol | ||||||
Function / homology | Function and homology information phosphotransferase activity, for other substituted phosphate groups / Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / phospholipid biosynthetic process / nucleotide binding / magnesium ion binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Archaeoglobus fulgidus (archaea) Renibacterium salmoninarum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å | ||||||
Authors | Clarke, O.B. / Tomasek, D.T. / Jorge, C.D. / Belcher Dufrisne, M. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Hendrickson, W.A. / Santos, H. / Mancia, F. | ||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis for phosphatidylinositol-phosphate biosynthesis. Authors: Clarke, O.B. / Tomasek, D. / Jorge, C.D. / Dufrisne, M.B. / Kim, M. / Banerjee, S. / Rajashankar, K.R. / Shapiro, L. / Hendrickson, W.A. / Santos, H. / Mancia, F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5d91.cif.gz | 158.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5d91.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d9/5d91 ftp://data.pdbj.org/pub/pdb/validation_reports/d9/5d91 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5d92C 4o6mS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36950.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Archaeoglobus fulgidus (archaea), (gene. exp.) Renibacterium salmoninarum (bacteria) Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126, ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235 Gene: AF_2299, RSal33209_2010 / Production host: Escherichia coli (E. coli) / References: UniProt: O27985, UniProt: A9WSF5 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-8K6 / #4: Chemical | ChemComp-MG / | #5: 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: 61.85 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 20% (v/v) PEG 400, 0.1 M MES pH 6.7, 0.2 M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97911 Å | |||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.5→103.92 Å / Num. obs: 16926 / % possible obs: 98.2 % / Redundancy: 19 % / Biso Wilson estimate: 43.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.063 / Net I/σ(I): 9.9 / Num. measured all: 320975 / Scaling rejects: 4 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4o6m Resolution: 2.501→14.976 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.76 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 180.02 Å2 / Biso mean: 72.6785 Å2 / Biso min: 27.04 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.501→14.976 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|