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Yorodumi- PDB-4qyp: The Crystal Structures of holo-wt human Cellular Retinol Binding ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qyp | ||||||
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Title | The Crystal Structures of holo-wt human Cellular Retinol Binding protein II (hCRBPII) bound to Retinal | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / beta barrel / transfer protein / kidney / liver / RETINOL-BINDING PROT | ||||||
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: 1.62 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 | 4qyp.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qyp.ent.gz | 99.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/4qyp ftp://data.pdbj.org/pub/pdb/validation_reports/qy/4qyp | HTTPS FTP |
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-Related structure data
Related structure data | 4qynC 4qztC 4qzuC 2rcqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 15597.452 Da / Num. of mol.: 4 / 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) / 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: 1.99 Å3/Da / Density % sol: 38.33 % |
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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: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 7, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. all: 76879 / Num. obs: 56034 / % possible obs: 83.9 % / Rmerge(I) obs: 0.32 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RCQ Resolution: 1.62→48.44 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.106 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.123 / 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: 21.059 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→48.44 Å
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Refine LS restraints |
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