+Open data
-Basic information
Entry | Database: PDB / ID: 7nl2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Xyn11 from Pseudothermotoga thermarum | ||||||
Components | Beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / xylan / xylanase / xylanases / enzyme / hemicelluloses / xylose / biopolymer / plants / Pseudothermotoga maritima / extremophilic protein / thermorresistant / thermostability / alkalinity / Glycoside Hydrolase Family 10. | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Pseudothermotoga thermarum DSM 5069 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
Citation | Journal: Comput Struct Biotechnol J / Year: 2021 Title: Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity Authors: Talens-Perales, D. / Jimenez-Ortega, E. / Sanchez-Torres, P. / Sanz-Aparicio, J. / Polaina, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7nl2.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7nl2.ent.gz | 132 KB | Display | PDB format |
PDBx/mmJSON format | 7nl2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/7nl2 ftp://data.pdbj.org/pub/pdb/validation_reports/nl/7nl2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5ofjS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
2 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 8 - 340 / Label seq-ID: 8 - 340
|
-Components
#1: Protein | Mass: 41407.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudothermotoga thermarum DSM 5069 (bacteria) Gene: Theth_1636 / Production host: Escherichia coli (E. coli) / Variant (production host): Rosetta2 / References: UniProt: F7YXD6, endo-1,4-beta-xylanase #2: Chemical | ChemComp-GOL / #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 53.48 % / Description: Prism bar shape |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10% PEG 3350, 0.2 M Proline, 0.1 M Hepes pH 7.5. Mother liquor solution was supplemented by 25% of glycerol to cryoprotect the crystal during the data collection. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2020 / Details: KB Mirrors |
Radiation | Monochromator: Si(111) channel-cut, cryocooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979257 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.63 Å / Num. obs: 81903 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.038 / Rrim(I) all: 0.098 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4456 / CC1/2: 0.882 / Rpim(I) all: 0.293 / Rrim(I) all: 0.745 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OFJ Resolution: 1.8→44.5 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.535 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 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 max: 93.11 Å2 / Biso mean: 26.006 Å2 / Biso min: 12.87 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→44.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 12176 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|