[English] 日本語
![](img/lk-miru.gif)
- PDB-7ud1: The Crystal Structure of Apo Monomer F57:H:H:H:R58 HCRBPII with H... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7ud1 | ||||||
---|---|---|---|---|---|---|---|
Title | The Crystal Structure of Apo Monomer F57:H:H:H:R58 HCRBPII with Histidine Insertion in the Hinge Loop Region at 1.3 Angstrom Resolution | ||||||
![]() | Retinol-binding protein 2 | ||||||
![]() | LIPID BINDING PROTEIN / LBP / CRBPII | ||||||
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: The Crystal Structure of Apo Monomer F57:H:H:H:R58 HCRBPII with Histidine Insertion in the Hinge Loop Region at 1.3 Angstrom Resolution Authors: Ghanbarpour, A. / Geiger, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 160.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 104.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 428.1 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rcqS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 16011.896 Da / Num. of mol.: 2 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.24 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, Sodium acetate, ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.32→29.09 Å / Num. obs: 55379 / % possible obs: 96.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.087 / Net I/σ(I): 27.9 |
Reflection shell | Resolution: 1.964→2.035 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 5345 / Rrim(I) all: 0.602 / % possible all: 93.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2RCQ Resolution: 1.32→29.09 Å / SU ML: 0.1369 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4963 Stereochemistry target values: GeoStd + Monomer Library + 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: 16.73 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→29.09 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 60.0223476086 Å / Origin y: -20.5987725934 Å / Origin z: 13.7485355522 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |