+Open data
-Basic information
Entry | Database: PDB / ID: 5nu7 | ||||||
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Title | Structure of human holo plasma RBP4 | ||||||
Components | Retinol-binding protein 4 | ||||||
Keywords | TRANSPORT PROTEIN / RBP4 / plasma retinol-binding protein / lipocalin / retinol | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Perduca, M. / Monaco, H.L. / Galliano, M. | ||||||
Citation | Journal: Biochim. Biophys. Acta / Year: 2018 Title: Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein. Authors: Perduca, M. / Nicolis, S. / Mannucci, B. / Galliano, M. / Monaco, H.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nu7.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nu7.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nu7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/5nu7 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nu7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ntyC 5nu2C 5nu6C 5nu8C 5nu9C 5nuaC 5nubC 1brpS 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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Unit cell |
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-Components
#1: Protein | Mass: 20984.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02753 |
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#2: Chemical | ChemComp-RTL / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 277 K / Method: microdialysis / Details: 4.5 M NaCl, 20 mM Na cacodylate, pH 6.8 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.16 Å / Num. obs: 46674 / % possible obs: 99.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.8 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BRP Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.135 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.232 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→30 Å
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Refine LS restraints |
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