[English] 日本語
Yorodumi- PDB-4az9: Crystal structure of phox homology domain of human sorting nexin 24 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4az9 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of phox homology domain of human sorting nexin 24 | ||||||
Components | SORTING NEXIN-24 | ||||||
Keywords | PROTEIN TRANSPORT | ||||||
Function / homology | Function and homology information phosphatidylinositol-5-phosphate binding / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-4-phosphate binding / cytoplasmic vesicle membrane / protein transport Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.75 Å | ||||||
Authors | Oberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. ...Oberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Phox Homology Domain of Human Sorting Nexin 24 Authors: Oberholzer, A.E. / Kiyani, W. / Krojer, T. / Shrestha, L. / von Delft, F. / Froese, D.S. / Chaikuad, A. / Raynor, J. / Arrowsmith, C. / Edwards, A. / Bountra, C. / Yue, W.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4az9.cif.gz | 110.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4az9.ent.gz | 91.5 KB | Display | PDB format |
PDBx/mmJSON format | 4az9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4az9_validation.pdf.gz | 449.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4az9_full_validation.pdf.gz | 451.1 KB | Display | |
Data in XML | 4az9_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 4az9_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/az/4az9 ftp://data.pdbj.org/pub/pdb/validation_reports/az/4az9 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15509.854 Da / Num. of mol.: 2 / Fragment: PHOX HOMOLOGY DOMAIN, RESIDUES 160-266 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9Y343 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.3 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 73 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 29, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→122.68 Å / Num. obs: 30020 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS Starting model: NONE Resolution: 1.75→122.66 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.213 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 22.959 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→122.66 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|