[English] 日本語
![](img/lk-miru.gif)
- PDB-7bm6: Structure-function analysis of a new PL17 oligoalginate lyase fro... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7bm6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT | |||||||||
![]() | Alginate lyase, family PL17 | |||||||||
![]() | HYDROLASE / alginate lyase / delta-guluronate complex / family PL17 / exo-acting marine enzyme | |||||||||
Function / homology | mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / Heparinase II/III-like / Heparinase II/III-like protein / Alginate lyase domain / Alginate lyase / Chondroitin AC/alginate lyase / periplasmic space / Alginate lyase, family PL17![]() | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Czjzek, M. / Roret, T. / Jouanneau, D. / Le Duff, N. / Jeudy, A. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT. Authors: Jouanneau, D. / Klau, L.J. / Larocque, R. / Jaffrennou, A. / Duval, G. / Le Duff, N. / Roret, T. / Jeudy, A. / Aachmann, F.L. / Czjzek, M. / Thomas, F. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 585.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 480.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 58.9 KB | Display | |
Data in CIF | ![]() | 87.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bjtSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 85059.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The active site tyrosine Y274 was mutated to alanine Y247A The N-terminal peptide (1-23) was not included in recombinant construction defined by electron density Source: (gene. exp.) ![]() Strain: DSM 12802 / CCUG 47099 / CIP 106680 / NCIMB 13871 / Dsij Gene: alyA3, zobellia_2624 / Production host: ![]() ![]() References: UniProt: G0LCA3, mannuronate-specific alginate lyase #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
---|
-Non-polymers , 4 types, 919 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 68 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: protein solution at 13.4 mg.ml-1, supplemented with 1.6 mM of oligo-mannuronate of DP3, was mixed with 0.2 micro-l of crystallization solution that contained 2.4 M sodium malonate (dibasic ...Details: protein solution at 13.4 mg.ml-1, supplemented with 1.6 mM of oligo-mannuronate of DP3, was mixed with 0.2 micro-l of crystallization solution that contained 2.4 M sodium malonate (dibasic monohydrate) and equilibrated against a reservoir containing 100 micro-l. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jan 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→45 Å / Num. obs: 137171 / % possible obs: 99.6 % / Redundancy: 21.16 % / CC1/2: 0.999 / Rpim(I) all: 0.054 / Rsym value: 0.12 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.16→2.21 Å / Redundancy: 18 % / Rmerge(I) obs: 1.57 / Num. unique obs: 7343 / CC1/2: 0.641 / Rpim(I) all: 0.356 / % possible all: 99.2 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7BJT Resolution: 2.16→45 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.495 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.27 Å2 / Biso mean: 33.489 Å2 / Biso min: 17.67 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.16→45 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.16→2.216 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|