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Yorodumi- PDB-4zh6: Crystal Structure of the Domain-Swapped Dimer Y60L mutant of Huma... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zh6 | ||||||
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Title | Crystal Structure of the Domain-Swapped Dimer Y60L mutant of Human Cellular Retinol Binding Protein II | ||||||
Components | Retinol-binding protein 2 | ||||||
Keywords | TRANSPORT PROTEIN / Domain-Swapped Dimer / Domain Swapping / Human Cellular Retinol Binding Protein II / Intracellular Lipid Binding Protein | ||||||
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: 1.5497 Å | ||||||
Authors | Assar, Z. / Nossoni, Z. / 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: Acta Crystallogr.,Sect.D / Year: 2014 Title: Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal. Authors: Nossoni, Z. / Assar, Z. / Yapici, I. / Nosrati, M. / Wang, W. / Berbasova, T. / Vasileiou, C. / Borhan, B. / Geiger, J. #2: 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 | 4zh6.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zh6.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zh6_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 4zh6_full_validation.pdf.gz | 435.3 KB | Display | |
Data in XML | 4zh6_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 4zh6_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/4zh6 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/4zh6 | HTTPS FTP |
-Related structure data
Related structure data | 4zcbC 4zguC 4zh9C 4zj0C 4zr2C 5dg4C 5dpqC 2rctS 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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Details | Dimer confirmed by gel filtration |
-Components
#1: Protein | Mass: 15547.437 Da / Num. of mol.: 1 / Mutation: Y60L 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 | ||
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#2: Chemical | #3: 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: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 4000 (40%), 0.1M Sodium Acetate pH 4.5, Ammonium Acetate 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.5497→50 Å / Num. obs: 21293 / % possible obs: 99.81 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 82.03 |
Reflection shell | Resolution: 1.5497→1.588 Å / Rmerge(I) obs: 0.695 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2RCT Resolution: 1.5497→31.837 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 23.4 / 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: 1.5497→31.837 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 2.6871 Å / Origin y: 36.2798 Å / Origin z: -3.1689 Å
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Refinement TLS group | Selection details: all |