[English] 日本語
![](img/lk-miru.gif)
- PDB-5g2t: BT1596 in complex with its substrate 4,5 unsaturated uronic acid ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5g2t | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-Glucosamine-2-N, 6-O-disulfate | ||||||||||||
![]() | 2-O GLYCOSAMINOGLYCAN SULFATASE | ||||||||||||
![]() | HYDROLASE / GLYCOSAMINOGLYCAN SULFATASE | ||||||||||||
Function / homology | ![]() glucuronate-2-sulfatase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / arylsulfatase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. ...Cartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. / Firbank, S.J. / Bolam, D.N. | ||||||||||||
![]() | ![]() Title: How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Authors: Cartmell, A. / Lowe, E.C. / Basle, A. / Firbank, S.J. / Ndeh, D.A. / Murray, H. / Terrapon, N. / Lombard, V. / Henrissat, B. / Turnbull, J.E. / Czjzek, M. / Gilbert, H.J. / Bolam, D.N. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 395.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 321 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 76.3 KB | Display | |
Data in CIF | ![]() | 111.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ak1C ![]() 4ak2C ![]() 5g2uC ![]() 5g2vC ![]() 3b5qS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54895.754 Da / Num. of mol.: 4 / Fragment: SULFATASE, UNP RESIDUE 13-481 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: VPI-5482 / Plasmid: PET28A / Production host: ![]() ![]() |
---|
-Sugars , 2 types, 4 molecules ![](data/chem/img/UAP.gif)
#2: Polysaccharide | Type: oligosaccharide / Mass: 577.470 Da / Num. of mol.: 2 / Source method: obtained synthetically #6: Sugar | |
---|
-Non-polymers , 4 types, 1213 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.56 % / Description: NONE |
---|---|
Crystal grow | Details: 14-20 % PEG 3350 0.2 M KCL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.4 Å / Num. obs: 153578 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 76.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3B5Q Resolution: 1.9→125.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.314 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.417 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→125.34 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|