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Yorodumi- PDB-7jx2: Cellular retinol-binding protein 2 (CRBP2) in complex with 2-palm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7jx2 | |||||||||
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Title | Cellular retinol-binding protein 2 (CRBP2) in complex with 2-palmitoylglycerol | |||||||||
Components | Retinol-binding protein 2 | |||||||||
Keywords | LIPID BINDING PROTEIN / palmitoylglycerol / monoacylglycerol / retinol-binding protein / lipid binding | |||||||||
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: 1.8 Å | |||||||||
Authors | Silvaroli, J.A. / Banarjee, S. / Golczak, M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Lipid Res. / Year: 2021 Title: Molecular basis for the interaction of cellular retinol binding protein 2 (CRBP2) with nonretinoid ligands. Authors: Silvaroli, J.A. / Plau, J. / Adams, C.H. / Banerjee, S. / Widjaja-Adhi, M.A.K. / 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 | 7jx2.cif.gz | 83.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7jx2.ent.gz | 60 KB | Display | PDB format |
PDBx/mmJSON format | 7jx2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7jx2_validation.pdf.gz | 671.5 KB | Display | wwPDB validaton report |
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Full document | 7jx2_full_validation.pdf.gz | 671.9 KB | Display | |
Data in XML | 7jx2_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 7jx2_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/7jx2 ftp://data.pdbj.org/pub/pdb/validation_reports/jx/7jx2 | HTTPS FTP |
-Related structure data
Related structure data | 7jvgC 7jvyC 7jwdC 7jwrC 7jz5C 7k3iC 6btiS 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: 16195.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21De / References: UniProt: P50120 |
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#2: Chemical | ChemComp-VLP / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris HCl, PEG 3350 22-28% |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→66.58 Å / Num. obs: 15466 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.072 / Rrim(I) all: 0.134 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.873 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 889 / CC1/2: 0.881 / Rpim(I) all: 0.554 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BTI Resolution: 1.8→46.31 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.44 / 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: 1.8→46.31 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: -4.0167 Å / Origin y: -10.3064 Å / Origin z: 15.5622 Å
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Refinement TLS group | Selection details: all |