+Open data
-Basic information
Entry | Database: PDB / ID: 5nu2 | ||||||
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Title | Structure of non-fluorescent human urine RBP4 | ||||||
Components | Retinol-binding protein 4 | ||||||
Keywords | TRANSPORT PROTEIN / RBP4 / urine retinol-binding protein / lipocalin / fatty acid | ||||||
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 / FOURIER SYNTHESIS / 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 | 5nu2.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nu2.ent.gz | 69.8 KB | Display | PDB format |
PDBx/mmJSON format | 5nu2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nu2_validation.pdf.gz | 664.9 KB | Display | wwPDB validaton report |
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Full document | 5nu2_full_validation.pdf.gz | 666.8 KB | Display | |
Data in XML | 5nu2_validation.xml.gz | 10.7 KB | Display | |
Data in CIF | 5nu2_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nu/5nu2 ftp://data.pdbj.org/pub/pdb/validation_reports/nu/5nu2 | HTTPS FTP |
-Related structure data
Related structure data | 5ntySC 5nu6C 5nu7C 5nu8C 5nu9C 5nuaC 5nubC 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-PLM / | ||
#3: Chemical | #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: 293 K / Method: vapor diffusion, hanging drop / Details: 4.3 M NaCl, 100 mM Hepes, pH 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 27, 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→56.49 Å / Num. obs: 44537 / % possible obs: 96.7 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 1.8 / % possible all: 96.3 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 5NTY Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 2.966 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054
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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: 41.007 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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