[English] 日本語
![](img/lk-miru.gif)
- PDB-6lzq: Chitin-specific solute binding protein from Vibrio harveyi in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6lzq | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Chitin-specific solute binding protein from Vibrio harveyi in complex with chitotriose. | |||||||||
![]() | Peptide ABC transporter, periplasmic peptide-binding protein | |||||||||
![]() | SUGAR BINDING PROTEIN / complex / chitin / periplasmic solute-binding protein / Vibrios | |||||||||
Function / homology | ![]() ATP-binding cassette (ABC) transporter complex / transmembrane transport / outer membrane-bounded periplasmic space Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kitaoku, Y. / Ubonbal, P. / Tran, L.T. / Robinson, R.C. / Suginta, W. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. Authors: Kitaoku, Y. / Fukamizo, T. / Kumsaoad, S. / Ubonbal, P. / Robinson, R.C. / Suginta, W. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 136.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 101.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 804.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 806 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 35.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lztC ![]() 6lzuC ![]() 6lzvC ![]() 6lzwC ![]() 7ebiC ![]() 7ebmC ![]() 5yqwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 61288.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: VME_26970 / Production host: ![]() ![]() |
---|---|
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / triacetyl-beta-chitotriose |
-Non-polymers , 5 types, 353 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.09 % |
---|---|
Crystal grow | Temperature: 293 K / Method: microbatch / pH: 6.5 Details: 1.63mM chitotriose, 0.06M Divalents (MgCl2, CaCl2), 0.1M Buffer System 1 (Imidazole, MES (acid)), pH 6.5, 30% v/v Precipitant Mix 2 (Ethylene glycol, PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99984 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 48470 / % possible obs: 92.2 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.085 / Rrim(I) all: 0.155 / Rsym value: 0.155 / Net I/σ(I): 8.79 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 1.114 / Num. unique obs: 2253 / CC1/2: 0.262 / Rpim(I) all: 0.765 / Rrim(I) all: 1.362 / Rsym value: 1.656 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5yqw Resolution: 1.8→36.531 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→36.531 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|