+Open data
-Basic information
Entry | Database: PDB / ID: 4av8 | ||||||
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Title | Kluyveromyces lactis Hsv2 complete loop 6CD | ||||||
Components | SVP1-LIKE PROTEIN 2 | ||||||
Keywords | LIPID BINDING PROTEIN | ||||||
Function / homology | Function and homology information nucleophagy / protein localization to phagophore assembly site / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / vacuolar membrane / extrinsic component of membrane / cytoplasmic vesicle membrane / protein transport / cytosol Similarity search - Function | ||||||
Biological species | KLUYVEROMYCES LACTIS (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 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 | 4av8.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4av8.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 4av8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4av8 ftp://data.pdbj.org/pub/pdb/validation_reports/av/4av8 | HTTPS FTP |
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-Related structure data
Related structure data | 4av9SC 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: 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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-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 PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9765 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→40 Å / Num. obs: 9859 / % possible obs: 99.5 % / Observed criterion σ(I): 5.1 / Redundancy: 9.5 % / Biso Wilson estimate: 102.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 3.35→3.45 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AV9 Resolution: 3.35→39.09 Å / SU ML: 0.6 / σ(F): 2 / Phase error: 23.81 / 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: 75.522 Å2 / ksol: 0.341 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.35→39.09 Å
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Refine LS restraints |
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LS refinement shell |
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