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Yorodumi- PDB-6bti: Crystal structure of human cellular retinol binding protein 2 (CR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bti | ||||||
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Title | Crystal structure of human cellular retinol binding protein 2 (CRBP2) in complex with N-arachidonoylethanolamine (AEA) | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | LIPID BINDING PROTEIN / endocannabinoid / N-arachidonoylethanolamine / anandamide / retinol / vitamin A | ||||||
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: 1.45 Å | ||||||
Authors | Silvaroli, J.A. / Blaner, W.S. / Lodowski, D.T. / Golczak, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: Retinol-binding protein 2 (RBP2) binds monoacylglycerols and modulates gut endocrine signaling and body weight. Authors: Lee, S.A. / Yang, K.J.Z. / Brun, P.J. / Silvaroli, J.A. / Yuen, J.J. / Shmarakov, I. / Jiang, H. / Feranil, J.B. / Li, X. / Lackey, A.I. / Krezel, W. / Leibel, R.L. / Libien, J. / Storch, J. ...Authors: Lee, S.A. / Yang, K.J.Z. / Brun, P.J. / Silvaroli, J.A. / Yuen, J.J. / Shmarakov, I. / Jiang, H. / Feranil, J.B. / Li, X. / Lackey, A.I. / Krezel, W. / Leibel, R.L. / Libien, J. / Storch, J. / Golczak, M. / Blaner, W.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bti.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bti.ent.gz | 65 KB | Display | PDB format |
PDBx/mmJSON format | 6bti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bt/6bti ftp://data.pdbj.org/pub/pdb/validation_reports/bt/6bti | HTTPS FTP |
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-Related structure data
Related structure data | 6bthC 4qypS 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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Unit cell |
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-Components
#1: Protein | Mass: 16195.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Cell line (production host): BL21 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P50120 #2: Chemical | #3: Chemical | #4: 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: 2.65 Å3/Da / Density % sol: 53.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M TrisHCl, PEG 3350 22-28%. / PH range: 7.5 - 8.5 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→53.45 Å / Num. obs: 59550 / % possible obs: 96.7 % / Redundancy: 6.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.038 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2870 / CC1/2: 0.68 / Rpim(I) all: 0.459 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4QYP Resolution: 1.45→44.131 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.14 / 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: 1.45→44.131 Å
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Refine LS restraints |
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LS refinement shell |
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