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Yorodumi- PDB-4wpc: Crystal structure of Rgd1p F-BAR domain in complex with inositol ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wpc | ||||||
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Title | Crystal structure of Rgd1p F-BAR domain in complex with inositol phosphate | ||||||
Components | RHO GTPase-activating protein RGD1 | ||||||
Keywords | LIPID BINDING PROTEIN / F-BAR domain / phospholipid binding / PROTEIN BINDING | ||||||
Function / homology | Function and homology information : / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / RHOA GTPase cycle / cellular bud / prospore membrane / actin cortical patch ...: / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / RHOA GTPase cycle / cellular bud / prospore membrane / actin cortical patch / phosphatidylinositol-5-phosphate binding / mating projection tip / phosphatidylinositol-3-phosphate binding / response to acidic pH / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to osmotic stress / Neutrophil degranulation / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / signal transduction / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å | ||||||
Authors | Moravcevic, K. / Lemmon, M.A. | ||||||
Citation | Journal: Structure / Year: 2015 Title: Comparison of Saccharomyces cerevisiae F-BAR Domain Structures Reveals a Conserved Inositol Phosphate Binding Site. Authors: Moravcevic, K. / Alvarado, D. / Schmitz, K.R. / Kenniston, J.A. / Mendrola, J.M. / Ferguson, K.M. / Lemmon, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4wpc.cif.gz | 210.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4wpc.ent.gz | 170.2 KB | Display | PDB format |
PDBx/mmJSON format | 4wpc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/4wpc ftp://data.pdbj.org/pub/pdb/validation_reports/wp/4wpc | HTTPS FTP |
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-Related structure data
Related structure data | 4wpeSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36879.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: RGD1, YBR260C, YBR1728 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P38339 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.61 Å3/Da / Density % sol: 73.3 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M citrate, pH 5.5, containing 0.1-0.2 M (NH4)2SO4 plus 10-20% (w/v) PEG3350 PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→50 Å / Num. obs: 19341 / % possible obs: 99.7 % / Redundancy: 4.2 % / Net I/σ(I): 14 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4WPE Resolution: 3.34→30.773 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.34→30.773 Å
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Refine LS restraints |
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LS refinement shell |
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