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- PDB-6vis: The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vis | ||||||
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Title | The Crystal Structure of Domain-Swapped Trimer Q108K:K40D:T53A:R58L:Q38F:Q4F:V62E Variant of HCRBPII | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / Domain Swapped Trimer / 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 | ![]() | 207.7 KB | Display | ![]() |
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PDB format | ![]() | 139.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 299.5 KB | Display | ![]() |
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Full document | ![]() | 299.4 KB | Display | |
Data in XML | ![]() | 1.3 KB | Display | |
Data in CIF | ![]() | 5.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vitC ![]() 6wnfC ![]() 6wnjC ![]() 6wp0C ![]() 6wp1C ![]() 6wp2C ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1
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Components
#1: Protein | Mass: 15578.421 Da / Num. of mol.: 3 / Mutation: Q108K, K40D, T53A, R58L, Q38F, Q4F, V62E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pET-11a (others) References: UniProt: P50120 #2: Chemical | #3: 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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: PEG 4000, Sodium acetate, ammonium acetate |
-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: Mar 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.788→48.13 Å / Num. obs: 10793 / % possible obs: 99.24 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.46 Å2 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.16 / Net I/σ(I): 17.14 |
Reflection shell | Resolution: 2.788→2.888 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.819 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 1015 / Rrim(I) all: 0.886 / % possible all: 93.81 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2rct Resolution: 2.79→48.13 Å / SU ML: 0.5222 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.4608 / Stereochemistry target values: CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.82 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→48.13 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: 51.7405525202 Å / Origin y: 24.9915336269 Å / Origin z: 30.3394018303 Å
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Refinement TLS group | Selection details: all |