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Yorodumi- PDB-4zj0: The crystal structure of monomer Q108K:K40L:Y60W CRBPII bound to ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zj0 | ||||||
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Title | The crystal structure of monomer Q108K:K40L:Y60W CRBPII bound to all-trans-retinal | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / domain swapping dimer | ||||||
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: 1.5 Å | ||||||
Authors | Nossoni, Z. / Assar, Z. / Wang, W. / Vasileiou, C. / Borhan, B. / Geiger, J.H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Structure / Year: 2016 Title: Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates. Authors: Assar, Z. / Nossoni, Z. / Wang, W. / Santos, E.M. / Kramer, K. / McCornack, C. / Vasileiou, C. / Borhan, B. / Geiger, J.H. #1: 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 | 4zj0.cif.gz | 76.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zj0.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 4zj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zj/4zj0 ftp://data.pdbj.org/pub/pdb/validation_reports/zj/4zj0 | HTTPS FTP |
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-Related structure data
Related structure data | 4zcbC 4zguC 4zh6C 4zh9C 4zr2C 5dg4C 5dpqC 2rcqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15605.519 Da / Num. of mol.: 2 / Fragment: UNP residues 2-134 / Mutation: K40L, Y60W, Q108K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2 / Plasmid: pET17b / 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 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG4000, 0.1M CH3COONa.3H2O, pH 4.6, 0.1M CH3COONH4 |
-Data collection
Diffraction | Mean temperature: 194 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→21.3 Å / Num. all: 41751 / Num. obs: 41751 / % possible obs: 92.8 % / Redundancy: 4.1 % / Net I/σ(I): 50.3 |
Reflection shell | Resolution: 1.5→1.52 Å / Mean I/σ(I) obs: 3.58 / % possible all: 68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2RCQ Resolution: 1.5→21.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.634 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 23.022 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→21.3 Å
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Refine LS restraints |
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