+Open data
-Basic information
Entry | Database: PDB / ID: 5nty | ||||||
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Title | Structure of non-fluorescent human plasma RBP4 | ||||||
Components | Retinol-binding protein 4 | ||||||
Keywords | TRANSPORT PROTEIN / RBP4 / plasma retinol-binding protein / lipocalin / fatty acid / signaling 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 / retinal binding / cardiac muscle tissue development / 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: 2 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 | 5nty.cif.gz | 90.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nty.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nty_validation.pdf.gz | 659.1 KB | Display | wwPDB validaton report |
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Full document | 5nty_full_validation.pdf.gz | 662.3 KB | Display | |
Data in XML | 5nty_validation.xml.gz | 10.3 KB | Display | |
Data in CIF | 5nty_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nt/5nty ftp://data.pdbj.org/pub/pdb/validation_reports/nt/5nty | HTTPS FTP |
-Related structure data
Related structure data | 5nu2C 5nu6C 5nu7C 5nu8C 5nu9C 5nuaC 5nubC 1brqS 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: 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-PLM / |
#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 | Density Matthews: 3.65 Å3/Da / Density % sol: 66.31 % |
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Crystal grow | Temperature: 279 K / Method: microdialysis / Details: 4.5M NaCl, 20mM Na cacodylate, pH 6.8 |
-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: Jul 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 19780 / % possible obs: 98.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.106 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1brq Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.939 / SU B: 10.31 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.133
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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: 55.543 Å2
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Refinement step | Cycle: 1 / Resolution: 2→30 Å
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Refine LS restraints |
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