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Yorodumi- PDB-5ha1: Crystal structure of human cellular retinol binding protein 1 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ha1 | |||||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with retinylamine | |||||||||
Components | Retinol-binding protein 1 | |||||||||
Keywords | RETINOL-BINDING PROTEIN / retinylamine / 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: 1.35 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 | 5ha1.cif.gz | 113.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ha1.ent.gz | 86.7 KB | Display | PDB format |
PDBx/mmJSON format | 5ha1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/5ha1 ftp://data.pdbj.org/pub/pdb/validation_reports/ha/5ha1 | HTTPS FTP |
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-Related structure data
Related structure data | 5h8tC 5h9aC 5hbsC 1crbS 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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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-RNE / ( |
#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: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 298 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: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→27.55 Å / Num. obs: 30442 / % possible obs: 100 % / Redundancy: 5.9 % / Rsym value: 0.0103 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.32→1.35 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.604 / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1CRB Resolution: 1.35→27.548 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34 / 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: 1.35→27.548 Å
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Refine LS restraints |
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LS refinement shell |
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