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- PDB-6on7: Crystal Structure of Apo Domain-Swapped Dimer Q108K:T51D:A28C:L36... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6on7 | ||||||
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Title | Crystal Structure of Apo Domain-Swapped Dimer Q108K:T51D:A28C:L36C Mutant of Human Cellular Retinol Binding Protein II | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / Retinol / iLBP / Protein Switch / CYTOSOLIC PROTEIN | ||||||
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: Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches. Authors: Ghanbarpour, A. / Pinger, C. / Esmatpour Salmani, R. / Assar, Z. / Santos, E.M. / Nosrati, M. / Pawlowski, K. / Spence, D. / Vasileiou, C. / Jin, X. / 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 | ![]() | 67.4 KB | Display | ![]() |
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PDB format | ![]() | 49 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.1 KB | Display | ![]() |
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Full document | ![]() | 430.7 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6e50C ![]() 6e51C ![]() 6e5eC ![]() 6e5qC ![]() 6e5rC ![]() 6e5sC ![]() 6e6lC ![]() 6e7mC ![]() 6mcuC ![]() 6mcvC ![]() 6mkvC ![]() 6mlbC ![]() 6on5C ![]() 6on8C ![]() 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 15634.538 Da / Num. of mol.: 2 / Mutation: Q108K,T51D,A28C,L36C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pBEN1-SGC (others) References: UniProt: P50120 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.39 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG4000, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97624 Å / Relative weight: 1 |
Reflection | Resolution: 1.981→31.47 Å / Num. obs: 17686 / % possible obs: 93 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.1 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.981→2.052 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2.81 / Num. unique obs: 1739 / Rrim(I) all: 0.468 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2RCT Resolution: 1.981→31.47 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.33 / 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: 1.981→31.47 Å
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Refine LS restraints |
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LS refinement shell |
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