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Yorodumi- PDB-5hbs: Crystal structure of human cellular retinol binding protein 1 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hbs | |||||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with all-trans-retinol at 0.89 angstrom. | |||||||||
Components | Retinol-binding protein 1 | |||||||||
Keywords | RETINOL-BINDING PROTEIN / vitamin A / retinol / binding protein | |||||||||
Function / homology | Function and homology information all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport ...all-trans-retinol binding / retinoic acid biosynthetic process / vitamin A metabolic process / retinoid binding / retinal binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / lipid homeostasis / fatty acid transport / Retinoid metabolism and transport / lipid droplet / fatty acid binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.89 Å | |||||||||
Authors | Golczak, M. / Arne, J.M. / Silvaroli, J.A. / Kiser, P.D. / Banerjee, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Ligand Binding Induces Conformational Changes in Human Cellular Retinol-binding Protein 1 (CRBP1) Revealed by Atomic Resolution Crystal Structures. Authors: Silvaroli, J.A. / Arne, J.M. / Chelstowska, S. / Kiser, P.D. / Banerjee, S. / Golczak, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hbs.cif.gz | 116.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hbs.ent.gz | 90.2 KB | Display | PDB format |
PDBx/mmJSON format | 5hbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5hbs_validation.pdf.gz | 609.2 KB | Display | wwPDB validaton report |
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Full document | 5hbs_full_validation.pdf.gz | 609.6 KB | Display | |
Data in XML | 5hbs_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5hbs_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hb/5hbs ftp://data.pdbj.org/pub/pdb/validation_reports/hb/5hbs | HTTPS FTP |
-Related structure data
Related structure data | 5h8tSC 5h9aC 5ha1C 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: 16568.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP1, CRBP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P09455 |
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#2: Chemical | ChemComp-RTL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.11 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Bis-Tris, 25% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.7293 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7293 Å / Relative weight: 1 |
Reflection | Resolution: 0.89→33.2 Å / Num. obs: 104073 / % possible obs: 98.7 % / Redundancy: 12.4 % / Rsym value: 0.088 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 0.89→0.94 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 3.2 / % possible all: 92.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H8T Resolution: 0.89→33.2 Å / SU ML: 0.05 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.69 / 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: 0.89→33.2 Å
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Refine LS restraints |
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LS refinement shell |
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