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Yorodumi- PDB-4exz: Crystal Structure of the Q108K:K40L Mutant of Cellular Retinol Bi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4exz | ||||||
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Title | Crystal Structure of the Q108K:K40L Mutant of Cellular Retinol Binding Protein Type II in Complex with All-trans-Retinal at 1.7 Angstrom Resolution | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / retinal complex / beta barrel | ||||||
Function / homology | Function and homology information vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.608 Å | ||||||
Authors | Nossoni, Z. / Geiger, J.H. | ||||||
Citation | Journal: Science / Year: 2012 Title: Tuning the electronic absorption of protein-embedded all-trans-retinal. Authors: Wang, W. / Nossoni, Z. / Berbasova, T. / Watson, C.T. / Yapici, I. / Lee, K.S. / Vasileiou, C. / Geiger, J.H. / Borhan, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4exz.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4exz.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 4exz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4exz_validation.pdf.gz | 890.9 KB | Display | wwPDB validaton report |
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Full document | 4exz_full_validation.pdf.gz | 900.3 KB | Display | |
Data in XML | 4exz_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4exz_validation.cif.gz | 21.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/4exz ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exz | HTTPS FTP |
-Related structure data
Related structure data | 4edeC 4eejC 4efgC 4gkcC 4ruuC 2rcqS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-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: 15581.497 Da / Num. of mol.: 2 / Mutation: Q108K:K40L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / References: UniProt: P50120 #2: Chemical | #3: Chemical | #4: 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: 2.02 Å3/Da / Density % sol: 39.06 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD |
Radiation | Monochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 |
Reflection | Resolution: 1.608→33.016 Å / Num. obs: 27686 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2RCQ Resolution: 1.608→33.016 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.025 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.677 Å2
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Refinement step | Cycle: LAST / Resolution: 1.608→33.016 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.608→1.649 Å / Total num. of bins used: 20
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