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Yorodumi- PDB-9bcb: Crystal structure of human cellular retinol binding protein 3 in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 9bcb | ||||||
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Title | Crystal structure of human cellular retinol binding protein 3 in complex with C11 TopFluor MG | ||||||
Components | Retinol-binding protein 5 | ||||||
Keywords | LIPID BINDING PROTEIN / Cellular-retinol binding protein / retinol / retinoids / lipid transport | ||||||
Function / homology | Function and homology information retinoid binding / retinal binding / retinol binding / fatty acid transport / fatty acid binding / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Golczak, M. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Interactom of cellular retinol binding protein 3. Authors: Golczak, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9bcb.cif.gz | 83.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9bcb.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9bcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9bcb_validation.pdf.gz | 741.4 KB | Display | wwPDB validaton report |
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Full document | 9bcb_full_validation.pdf.gz | 746.5 KB | Display | |
Data in XML | 9bcb_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 9bcb_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/9bcb ftp://data.pdbj.org/pub/pdb/validation_reports/bc/9bcb | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 16419.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE / References: UniProt: P82980 #2: Chemical | ChemComp-A1ALJ / | Mass: 506.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H41BF2N2O4 / Feature type: SUBJECT OF INVESTIGATION #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.07 Å3/Da / Density % sol: 40.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M sodium malonate, pH 5.0 and 20% PEG 3350 (w/v) |
-Data collection
Diffraction | Mean temperature: 85 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→19.6 Å / Num. obs: 47122 / % possible obs: 98.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 17.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.032 / Rrim(I) all: 0.059 / Χ2: 1 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.45→1.47 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2330 / CC1/2: 0.807 / Rpim(I) all: 0.535 / Rrim(I) all: 0.764 / Χ2: 1.02 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.6 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→19.6 Å
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Refine LS restraints |
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LS refinement shell |
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