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Yorodumi- PDB-4xur: Structure of the CBM22-2 xylan-binding domain from Paenibacillus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xur | |||||||||
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Title | Structure of the CBM22-2 xylan-binding domain from Paenibacillus barcinonensis Xyn10C in complex with xylotetraose | |||||||||
Components | Endo-1,4-beta-xylanase C | |||||||||
Keywords | SUGAR BINDING PROTEIN / Binding Site / Carbohydrates / Enzyme Stability / Substrate Specificity / Endo-1 / 4-beta-xylanase / Xylan-binding domain / Thermophilic enzymes / Thermostabilizing Domains / Xylotetraose | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding Similarity search - Function | |||||||||
Biological species | Paenibacillus barcinonensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | |||||||||
Authors | Sainz-Polo, M.A. / Sanz-Aparicio, J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xur.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xur.ent.gz | 86.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4xur_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 4xur_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4xur_validation.xml.gz | 20 KB | Display | |
Data in CIF | 4xur_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/4xur ftp://data.pdbj.org/pub/pdb/validation_reports/xu/4xur | HTTPS FTP |
-Related structure data
Related structure data | 4w8lC 4xunSC 4xuoC 4xupC 4xuqC 4xutC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 172 - 332 / Label seq-ID: 14 - 174
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 19920.992 Da / Num. of mol.: 3 / Fragment: UNP residues 186-366 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus barcinonensis (bacteria) / Gene: xynC / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / References: UniProt: O69230, endo-1,4-beta-xylanase |
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-Sugars , 4 types, 5 molecules
#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose |
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#3: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylobiose |
#4: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose |
#6: Sugar |
-Non-polymers , 2 types, 97 molecules
#5: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.18 % |
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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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å | |||||||||||||||
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: 0.8729 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.67→33.55 Å / Num. obs: 54496 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Rmerge(I) obs: 0.091 / Rsym value: 0.042 / Net I/av σ(I): 6.1 / Net I/σ(I): 13.1 / Num. measured all: 307899 | |||||||||||||||
Reflection shell | Resolution: 1.67→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 3.4 / Num. unique all: 7920 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XUN Resolution: 1.67→33.55 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.283 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.019 / ESU R Free: 0.019 / 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: 16.313 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→33.55 Å
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Refine LS restraints |
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