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Yorodumi- PDB-4o9s: Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o9s | |||||||||
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Title | Crystal structure of Retinol-Binding Protein 4 (RBP4)in complex with a non-retinoid ligand | |||||||||
Components | Retinol-binding protein 4 | |||||||||
Keywords | PROTEIN BINDING / retinol binding / Disease mutation / Retinol-binding / Secreted / Sensory transduction / Transport / Vision / Vitamin A / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation ...Retinoid metabolism disease events / urinary bladder development / embryonic retina morphogenesis in camera-type eye / retinol transport / female genitalia morphogenesis / retinol transmembrane transporter activity / embryonic organ morphogenesis / maintenance of gastrointestinal epithelium / embryonic skeletal system development / negative regulation of cardiac muscle cell proliferation / eye development / heart trabecula formation / cardiac muscle tissue development / retinal binding / retinol metabolic process / retinol binding / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / positive regulation of immunoglobulin production / response to retinoic acid / Retinoid metabolism and transport / visual perception / gluconeogenesis / lung development / positive regulation of insulin secretion / glucose homeostasis / heart development / extracellular space / extracellular exosome / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||
Authors | Wang, Z. / Johnstone, S. / Walker, N.P. | |||||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2014 Title: Structure-assisted discovery of the first non-retinoid ligands for Retinol-Binding Protein 4. Authors: Wang, Y. / Connors, R. / Fan, P. / Wang, X. / Wang, Z. / Liu, J. / Kayser, F. / Medina, J.C. / Johnstone, S. / Xu, H. / Thibault, S. / Walker, N. / Conn, M. / Zhang, Y. / Liu, Q. / Grillo, M. ...Authors: Wang, Y. / Connors, R. / Fan, P. / Wang, X. / Wang, Z. / Liu, J. / Kayser, F. / Medina, J.C. / Johnstone, S. / Xu, H. / Thibault, S. / Walker, N. / Conn, M. / Zhang, Y. / Liu, Q. / Grillo, M.P. / Motani, A. / Coward, P. / Wang, Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4o9s.cif.gz | 90.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4o9s.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 4o9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o9/4o9s ftp://data.pdbj.org/pub/pdb/validation_reports/o9/4o9s | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 24958.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP4, PRO2222 / Production host: Escherichia coli (E. coli) / References: UniProt: P02753 |
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-Non-polymers , 5 types, 263 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1M ammonium phosphate dibasic, 0.1M imidazole, 0.2M sodium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 27, 2007 |
Radiation | Monochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→63 Å / Num. all: 22054 / Num. obs: 22050 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.894 / SU B: 7.852 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.345 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.782 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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