+Open data
-Basic information
Entry | Database: PDB / ID: 4av9 | ||||||
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Title | Kluyveromyces lactis Hsv2 | ||||||
Components | SVP1-LIKE PROTEIN 2 | ||||||
Keywords | LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information vacuolar membrane / cytoplasmic vesicle membrane / autophagy / protein transport Similarity search - Function | ||||||
Biological species | KLUYVEROMYCES LACTIS (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å | ||||||
Authors | Krick, R. / Busse, R.A. / Scacioc, A. / Stephan, M. / Janshoff, A. / Thumm, M. / Kuhnel, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Structural and Functional Characterization of the Two Phosphoinositide Binding Sites of Proppins, a Beta-Propeller Protein Family. Authors: Krick, R. / Busse, R.A. / Scacioc, A. / Stephan, M. / Janshoff, A. / Thumm, M. / Kuhnel, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4av9.cif.gz | 74.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4av9.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 4av9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4av9 ftp://data.pdbj.org/pub/pdb/validation_reports/av/4av9 | HTTPS FTP |
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-Related 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: 39219.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) KLUYVEROMYCES LACTIS (yeast) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q6CN23 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 70 % / Description: NONE |
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Crystal grow | pH: 6.5 / Details: 1.6 M MGSO4, 0.1 M MES PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0015 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0015 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 14269 / % possible obs: 99.6 % / Observed criterion σ(I): 3 / Redundancy: 8.4 % / Biso Wilson estimate: 84.52 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 3→3.15 Å / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.9 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 3.001→56.226 Å / SU ML: 0.89 / σ(F): 2.01 / Phase error: 24.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.339 Å2 / ksol: 0.353 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.7 Å2
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Refinement step | Cycle: LAST / Resolution: 3.001→56.226 Å
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Refine LS restraints |
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LS refinement shell |
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