[English] 日本語
![](img/lk-miru.gif)
- PDB-6vit: The Crystal Structure of Apo Domain-Swapped dimer Q108K:T51D:I32C... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6vit | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Apo Domain-Swapped dimer Q108K:T51D:I32C Variant of HCRBPII with an Engineered Disulfide Bond | ||||||
![]() | 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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 80.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 49.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 248.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 248.3 KB | Display | |
Data in XML | ![]() | 941 B | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6visC ![]() 6wnfC ![]() 6wnjC ![]() 6wp0C ![]() 6wp1C ![]() 6wp2C ![]() 2rctS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 133 / Label seq-ID: 1 - 133
|
-
Components
#1: Protein | Mass: 15602.474 Da / Num. of mol.: 2 / Mutation: Q108K, T51D, I32C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: Bacterial expression vector pET-11a (others) References: UniProt: P50120 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.2 Å3/Da / Density % sol: 70.74 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: citric acid, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 17, 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: 3.2→50 Å / Num. obs: 8637 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 78.05 Å2 / Rmerge(I) obs: 0.2 / Rrim(I) all: 0.21 / Net I/σ(I): 13.85 |
Reflection shell | Resolution: 3.2→3.42 Å / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 843 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2rct Resolution: 3.2→38.48 Å / SU ML: 0.5048 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.0483 / Stereochemistry target values: CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 70.86 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→38.48 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|