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- PDB-6y0h: High resolution structure of GH11 xylanase from Nectria haematococca -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y0h | ||||||
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Title | High resolution structure of GH11 xylanase from Nectria haematococca | ||||||
![]() | Endo-1,4-beta-xylanase | ||||||
![]() | HYDROLASE / Xylanase / Atomic resolution / Nectria haematococca | ||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Andaleeb, H. / Betzel, C. / Perbandt, M. / Brognaro, H. | ||||||
![]() | ![]() Title: High-resolution crystal structure and biochemical characterization of a GH11 endoxylanase from Nectria haematococca. Authors: Andaleeb, H. / Ullah, N. / Falke, S. / Perbandt, M. / Brognaro, H. / Betzel, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 101.6 KB | Display | ![]() |
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PDB format | ![]() | 77.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.3 KB | Display | ![]() |
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Full document | ![]() | 409.1 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jrmS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 20917.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: endo-1,4-beta-xylanase activity Source: (gene. exp.) ![]() Gene: NECHADRAFT_106153 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 1 M Ammonium sulphate,100mM Sodium citrate |
-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: Dec 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1→34.67 Å / Num. obs: 82307 / % possible obs: 93.3 % / Redundancy: 3.2 % / CC1/2: 0.99 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1→1.06 Å / Num. unique obs: 11904 / CC1/2: 0.85 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5JRM Resolution: 1→34.67 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.897 / SU ML: 0.02 / Cross valid method: FREE R-VALUE / ESU R: 0.026 / ESU R Free: 0.025 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.58 Å2 / Biso mean: 9.386 Å2 / Biso min: 4.42 Å2
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Refinement step | Cycle: final / Resolution: 1→34.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1→1.023 Å / Rfactor Rfree error: 0
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