[English] 日本語
![](img/lk-miru.gif)
- PDB-6z5z: The RSL-R6 - sulfonato-calix[8]arene complex, P213 form, TRIS-HCl... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6z5z | ||||||
---|---|---|---|---|---|---|---|
Title | The RSL-R6 - sulfonato-calix[8]arene complex, P213 form, TRIS-HCl pH 8.5 | ||||||
![]() | Fucose-binding lectin protein | ||||||
![]() | SUGAR BINDING PROTEIN / calixarene / protein framework / cage / crystal engineering / molecular glue / synthetic receptor / macrocycle / biomaterial | ||||||
Function / homology | Fucose-specific lectin / Fungal fucose-specific lectin / carbohydrate binding / metal ion binding / beta-D-fructopyranose / sulfonato-calix[8]arene / Fucose-binding lectin protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramberg, K. / Engilberge, S. / Crowley, P.B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Facile Fabrication of Protein-Macrocycle Frameworks. Authors: Ramberg, K.O. / Engilberge, S. / Skorek, T. / Crowley, P.B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 918.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 919.1 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6z5gC ![]() 6z5mC ![]() 6z5pC ![]() 6z5qC ![]() 6z5wC ![]() 6z5xC ![]() 6z60C ![]() 6z62C ![]() 7alfC ![]() 7algC ![]() 2bt9S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 9817.604 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: RSL-R6 is an RSL mutant with all three lysines mutated to arginines (K25R, K34R, K83R). Source: (gene. exp.) ![]() Gene: E7Z57_08365, RSP795_21825, RSP822_19650, RUN39_v1_50103 Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-EVB / | ||||
#3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 31.9 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M TRIS-HCl pH 8.5, 1.6 M Ammonium sulfate, 0.2 M Lithium sulfate, 0.04 M sulfonato-calix[8]arene, 0.005 M D-fructose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→45.13 Å / Num. obs: 33221 / % possible obs: 100 % / Redundancy: 36.9 % / CC1/2: 0.998 / Rpim(I) all: 0.027 / Rrim(I) all: 0.168 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 23.1 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1632 / CC1/2: 0.772 / Rpim(I) all: 0.461 / Rrim(I) all: 2.236 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2BT9 Resolution: 1.124→45.128 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.94 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.42 Å2 / Biso mean: 14.3383 Å2 / Biso min: 5.62 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.124→45.128 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
|