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Open data
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Basic information
Entry | Database: PDB / ID: 7nl2 | ||||||
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Title | Structure of Xyn11 from Pseudothermotoga thermarum | ||||||
![]() | Beta-xylanase | ||||||
![]() | HYDROLASE / Glycoside hydrolase / xylan / xylanase / xylanases / enzyme / hemicelluloses / xylose / biopolymer / plants / Pseudothermotoga maritima / extremophilic protein / thermorresistant / thermostability / alkalinity / Glycoside Hydrolase Family 10. | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jimenez-Ortega, E. / Sanz-Aparicio, J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.3 KB | Display | ![]() |
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PDB format | ![]() | 132 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 336.6 KB | Display | ![]() |
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Full document | ![]() | 340.4 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ofjS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / 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: _ / Auth seq-ID: 8 - 340 / Label seq-ID: 8 - 340
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Components
#1: Protein | Mass: 41407.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: Theth_1636 / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Sugar | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 53.48 % / Description: Prism bar shape |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refinement step | Cycle: final / Resolution: 1.8→44.5 Å
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Refine LS restraints |
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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
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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