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Yorodumi- PDB-7nwp: A carbohydrate binding module family 9 (CBM9) from Caldicellulosi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nwp | |||||||||||||||
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Title | A carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjansonii in complex with cellobiose | |||||||||||||||
Components | Beta-xylanaseXylanase | |||||||||||||||
Keywords | SUGAR BINDING PROTEIN / CARBOHYDRATE BINDING MODULE | |||||||||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process / carbohydrate binding Similarity search - Function | |||||||||||||||
Biological species | Caldicellulosiruptor kristjanssonii | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.163 Å | |||||||||||||||
Authors | Krska, D. / Mazurkewich, S. / Navarro Poulsen, J. / Larsbrink, J. / Lo Leggio, L. | |||||||||||||||
Funding support | Sweden, Denmark, 4items
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Citation | Journal: Biochemistry / Year: 2021 Title: Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii . Authors: Krska, D. / Mazurkewich, S. / Brown, H.A. / Theibich, Y. / Poulsen, J.N. / Morris, A.L. / Koropatkin, N.M. / Lo Leggio, L. / Larsbrink, J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nwp.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nwp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7nwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nw/7nwp ftp://data.pdbj.org/pub/pdb/validation_reports/nw/7nwp | HTTPS FTP |
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-Related structure data
Related structure data | 7nn3C 7nwnC 7nwoC 7nwqC 1i8uS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules AAA
#1: Protein | Mass: 24645.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldicellulosiruptor kristjanssonii (strain ATCC 700853 / DSM 12137 / I77R1B) (bacteria) Strain: ATCC 700853 / DSM 12137 / I77R1B / Gene: Calkr_2245 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: E4S6E9, endo-1,4-beta-xylanase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-4)-beta-D-glucopyranose |
-Non-polymers , 4 types, 118 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.4 Å3/Da / Density % sol: 72.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 0.1 M phosphate-citrate and 40% polyethylene glycol 300 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.163→46.365 Å / Num. obs: 23991 / % possible obs: 99.95 % / Redundancy: 78.5 % / CC1/2: 1 / Net I/σ(I): 34.46 |
Reflection shell | Resolution: 2.163→2.24 Å / Num. unique obs: 2348 / CC1/2: 0.542 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1i8u Resolution: 2.163→46.365 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.15 / SU B: 4.33 / SU ML: 0.103 / Average fsc free: 0.9325 / Average fsc overall: 0.9459 / Average fsc work: 0.9474 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.14 / Details: Hydrogens have not been used
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.546 Å2
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Refinement step | Cycle: LAST / Resolution: 2.163→46.365 Å
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Refine LS restraints |
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LS refinement shell |
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