[English] 日本語
![](img/lk-miru.gif)
- PDB-6qi7: Engineered beta-lactoglobulin: variant L39Y in complex with endog... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6qi7 | ||||||
---|---|---|---|---|---|---|---|
Title | Engineered beta-lactoglobulin: variant L39Y in complex with endogenous ligand | ||||||
![]() | Beta-lactoglobulin | ||||||
![]() | TRANSPORT PROTEIN / lactoglobulin / lipocalin / mutant | ||||||
Function / homology | ![]() retinol binding / long-chain fatty acid binding / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Loch, J.I. / Siuda, M.K. / Lewinski, K. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-based design approach to rational site-directed mutagenesis of beta-lactoglobulin. Authors: Bonarek, P. / Loch, J.I. / Tworzydlo, M. / Cooper, D.R. / Milto, K. / Wrobel, P. / Kurpiewska, K. / Lewinski, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 76.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 55.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 572.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 573.1 KB | Display | |
Data in XML | ![]() | 8.6 KB | Display | |
Data in CIF | ![]() | 10.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qi6C ![]() 6qpdC ![]() 6qpeC ![]() 6rwpC ![]() 6rwqC ![]() 6rwrC ![]() 6rytC ![]() 6xveC ![]() 5htdS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18351.191 Da / Num. of mol.: 1 / Mutation: L1A, I2S, L39Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-PLM / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.60 M (NH4)2SO4 in 0.1 M Tris-HCl pH 7.1 |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å | ||||||||||||||||||||||||
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Mar 25, 2015 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.5→14.75 Å / Num. obs: 6635 / % possible obs: 99.4 % / Redundancy: 3.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Net I/σ(I): 9 / Num. measured all: 21453 / Scaling rejects: 198 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5HTD Resolution: 2.5→14.75 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.9 / SU B: 20.625 / SU ML: 0.222 / SU R Cruickshank DPI: 0.5573 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.557 / ESU R Free: 0.31 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.27 Å2 / Biso mean: 45.585 Å2 / Biso min: 21.82 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→14.75 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.563 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -12.0338 Å / Origin y: -10.6984 Å / Origin z: -14.5555 Å
|