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Yorodumi- PDB-4qzu: Crystal Structure of wild type Human Cellular Retinol Binding Pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qzu | ||||||
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Title | Crystal Structure of wild type Human Cellular Retinol Binding Protein II (hCRBPII) bound to retinol at 11 KeV beam energy | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | PROTEIN BINDING / Retinol / Human Cellular Retinol Binding Protein II / intracellular lipid binding protein / X-ray flux / X-ray damage / Retinal / Retinoid Chaperones | ||||||
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: 1.5 Å | ||||||
Authors | Assar, Z. / Geiger, J.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 | 4qzu.cif.gz | 249.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qzu.ent.gz | 202.2 KB | Display | PDB format |
PDBx/mmJSON format | 4qzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/4qzu ftp://data.pdbj.org/pub/pdb/validation_reports/qz/4qzu | HTTPS FTP |
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-Related structure data
Related structure data | 4qynC 4qypC 4qztC 2rctS 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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2 |
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3 |
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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 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: Chemical | ChemComp-GOL / | #5: 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: 1.96 Å3/Da / Density % sol: 37.17 % |
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Crystal grow | Temperature: 298 K / pH: 4.5 Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.496→34.66 Å / Num. obs: 76284 / % possible obs: 95.2 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 26.45 |
Reflection shell | Resolution: 1.5→1.51 Å / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.41 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCT Resolution: 1.5→34.66 Å / SU ML: 0.18 / σ(F): 1.97 / Phase error: 23.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→34.66 Å
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Refine LS restraints |
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LS refinement shell |
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