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- PDB-6wp2: The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q10... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wp2 | ||||||
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Title | The Crystal Structure of Apo Zinc-Bound Domain Swapped-Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:F57H Variant of HCRBPII | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / iLBP | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ghanbarpour, A. / Geiger, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering. Authors: Ghanbarpour, A. / Santos, E.M. / Pinger, C. / Assar, Z. / Hossaini Nasr, S. / Vasileiou, C. / Spence, D. / Borhan, B. / Geiger, J.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.9 KB | Display | ![]() |
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PDB format | ![]() | 73.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.4 MB | Display | ![]() |
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Full document | ![]() | 2.4 MB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6visC ![]() 6vitC ![]() 6wnfC ![]() 6wnjC ![]() 6wp0C ![]() 6wp1C ![]() 2rctS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15539.413 Da / Num. of mol.: 3 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F, F57H Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium iodide, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→50 Å / Num. obs: 15764 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 49.46 Å2 / CC1/2: 0.898 / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.166 / Net I/σ(I): 27 |
Reflection shell | Resolution: 2.47→2.52 Å / Rmerge(I) obs: 1.1 / Num. unique obs: 3092 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RCT Resolution: 2.48→47.17 Å / SU ML: 0.3458 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.2664
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.93 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.48→47.17 Å
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Refine LS restraints |
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LS refinement shell |
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