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Yorodumi- PDB-4qyn: The Crystal Structures of holo-wt human Cellular Retinol Binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qyn | ||||||
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Title | The Crystal Structures of holo-wt human Cellular Retinol Binding protein II (hCRBPII) bound to Retinol | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / transfer protein / kidney / lover | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å | ||||||
Authors | Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal. Authors: Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qyn.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qyn.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qyn_validation.pdf.gz | 836.9 KB | Display | wwPDB validaton report |
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Full document | 4qyn_full_validation.pdf.gz | 869.6 KB | Display | |
Data in XML | 4qyn_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4qyn_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qyn ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qyn | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15597.452 Da / Num. of mol.: 2 / Fragment: transfer protein Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pet17b / Production host: Escherichia coli (E. coli) / Strain (production host): vector / References: UniProt: P50120 #2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Water | ChemComp-HOH / | |
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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: 2.24 Å3/Da / Density % sol: 45.1 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.6 Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M ammonium acetate , pH 4.6, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→50 Å / Num. all: 306503 / Num. obs: 87302 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.19→25.28 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.003 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso mean: 13.634 Å2
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Refinement step | Cycle: LAST / Resolution: 1.19→25.28 Å
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LS refinement shell | Resolution: 1.189→1.22 Å / Total num. of bins used: 20
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