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- PDB-4xun: Structure of the CBM22-2 xylan-binding domain from Paenibacillus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xun | ||||||
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Title | Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C | ||||||
![]() | Endo-1,4-beta-xylanase C | ||||||
![]() | SUGAR BINDING PROTEIN / ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sainz-Polo, M.A. / Sanz-Aparicio, J. | ||||||
![]() | ![]() Title: Exploring Multimodularity in Plant Cell Wall Deconstruction: STRUCTURAL AND FUNCTIONAL ANALYSIS OF Xyn10C CONTAINING THE CBM22-1-CBM22-2 TANDEM. Authors: Sainz-Polo, M.A. / Gonzalez, B. / Menendez, M. / Pastor, F.I. / Sanz-Aparicio, J. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of Paenibacillus barcinonensis xylanase 10C containing the CBM22-1-CBM22-2 tandem. Authors: Sainz-Polo, M.A. / Gonzalez, B. / Pastor, F.I. / Sanz-Aparicio, 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 | ![]() | 112.8 KB | Display | ![]() |
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PDB format | ![]() | 85.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4w8lC ![]() 4xuoC ![]() 4xupC ![]() 4xuqC ![]() 4xurC ![]() 4xutC ![]() 1dyoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 0 / Auth seq-ID: 172 - 332 / Label seq-ID: 14 - 174
NCS ensembles :
NCS oper:
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Components
#1: Protein | Mass: 19920.992 Da / Num. of mol.: 3 / Fragment: UNP residues 186-336 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.85M Sodium malonate. Ratio protein/precipitant=0.5/1 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 14, 2013 | |||||||||||||||
Radiation | Monochromator: Horizontally side diffracting Silicon 111 crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.75→33.45 Å / Num. obs: 46784 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.8 % / Biso Wilson estimate: 12.643 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.043 / Net I/av σ(I): 13.4 / Net I/σ(I): 5.8 / Num. measured all: 272776 | |||||||||||||||
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6810 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1dyo Resolution: 1.75→33.45 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.824 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.021 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 17.693 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→33.45 Å
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Refine LS restraints |
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