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Yorodumi- PDB-3fmz: Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex ... -
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-Basic information
Entry | Database: PDB / ID: 3fmz | ||||||
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Title | Crystal Structure of Retinol-Binding Protein 4 (RBP4) in complex with non-retinoid ligand | ||||||
Components | Retinol-binding protein 4 | ||||||
Keywords | TRANSPORT PROTEIN / retinol binding / Disease mutation / Retinol-binding / Secreted / Sensory transduction / Transport / Vision / Vitamin A | ||||||
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 / positive regulation of immunoglobulin production / Retinoid cycle disease events / The canonical retinoid cycle in rods (twilight vision) / uterus development / vagina development / 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 / Resolution: 2.9 Å | ||||||
Authors | Wang, Z. / Johnstone, S. / Walker, N.P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Identification and Characterization of a Non-retinoid Ligand for Retinol-binding Protein 4 Which Lowers Serum Retinol-binding Protein 4 Levels in Vivo. Authors: Motani, A. / Wang, Z. / Conn, M. / Siegler, K. / Zhang, Y. / Liu, Q. / Johnstone, S. / Xu, H. / Thibault, S. / Wang, Y. / Fan, P. / Connors, R. / Le, H. / Xu, G. / Walker, N. / Shan, B. / Coward, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fmz.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fmz.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fmz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fm/3fmz ftp://data.pdbj.org/pub/pdb/validation_reports/fm/3fmz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 24620.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP4, PRO2222 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02753 #2: Chemical | #3: 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: 2.52 Å3/Da / Density % sol: 51.19 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion / pH: 6.5 Details: 0.4M Mg formate, 0.1M GndHCl, 0.1M Bis-Tris 6.5, vapor diffusion, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.999 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2007 / Details: 3X3 CCD ARRAY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL, SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→73.521 Å / Num. obs: 10890 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 52.465 Å2 / Rmerge(I) obs: 0.125 / Rsym value: 0.125 / Net I/σ(I): 5.773 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.795 / WRfactor Rfree: 0.259 / WRfactor Rwork: 0.203 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.826 / SU B: 16.978 / SU ML: 0.331 / SU Rfree: 0.445 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.445 / 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 max: 45.52 Å2 / Biso mean: 25.789 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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