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Yorodumi- PDB-6e5t: Crystal structure of human cellular retinol binding protein 1 in ... -
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-Basic information
Entry | Database: PDB / ID: 6e5t | ||||||
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Title | Crystal structure of human cellular retinol binding protein 1 in complex with abnormal-cannabidiorcin (Abn-CBDO) | ||||||
Components | Retinol-binding protein 1 | ||||||
Keywords | LIPID BINDING PROTEIN / vitamin A / retinol / abn-CBDO / abnormal cannabidiorcin | ||||||
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: 1.55 Å | ||||||
Authors | Silvaroli, J.A. / Horwitz, S. / Banerjee, S. / Kiser, P.D. / Golczak, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: Abnormal Cannabidiol Modulates Vitamin A Metabolism by Acting as a Competitive Inhibitor of CRBP1. Authors: Silvaroli, J.A. / Widjaja-Adhi, M.A.K. / Trischman, T. / Chelstowska, S. / Horwitz, S. / Banerjee, S. / Kiser, P.D. / Blaner, W.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 | 6e5t.cif.gz | 113.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e5t.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e5t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e5t_validation.pdf.gz | 753.1 KB | Display | wwPDB validaton report |
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Full document | 6e5t_full_validation.pdf.gz | 753 KB | Display | |
Data in XML | 6e5t_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6e5t_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/6e5t ftp://data.pdbj.org/pub/pdb/validation_reports/e5/6e5t | HTTPS FTP |
-Related structure data
Related structure data | 6e5lC 6e5wC 6e6kC 6e6mC 5h8tS 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-HVJ / ( |
#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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 m BisTris, pH 5.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→46.04 Å / Num. obs: 20911 / % possible obs: 99.2 % / Redundancy: 11.9 % / CC1/2: 1 / Rpim(I) all: 0.039 / Rsym value: 0.092 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.55→1.58 Å / Mean I/σ(I) obs: 2.9 / Num. unique all: 1037 / CC1/2: 0.66 / Rpim(I) all: 0.36 / Rsym value: 0.83 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5H8T Resolution: 1.55→34.586 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.46
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→34.586 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.8424 Å / Origin y: 42.2397 Å / Origin z: 102.3174 Å
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Refinement TLS group | Selection details: all |