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Yorodumi- PDB-3cuh: Cellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cuh | ||||||
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Title | Cellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex with cellotriose-like isofagomine | ||||||
Components | Exo-beta-1,4-glucanase | ||||||
Keywords | HYDROLASE / CEX / XYLANASE / Isofagomine inhibitor / TIM BARREL / Glycosidase | ||||||
Function / homology | Function and homology information cellulose 1,4-beta-cellobiosidase (non-reducing end) / cellulose 1,4-beta-cellobiosidase activity / polysaccharide binding / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Cellulomonas fimi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.89 Å | ||||||
Authors | Kuntz, D.A. / Saul, M. / Rose, D.R. | ||||||
Citation | Journal: to be published Title: Probing the binding sites of Family 10 and 11 Xylanases with extended Oligosaccharides Authors: Poon, D.K.Y. / D'Angelo, I.D. / Kuntz, D.A. / Kantner, T. / Ludkiwzek, M.L. / Tarling, C. / Rose, D.R. / Saul, M. / McIntosh, L.P. / Withers, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cuh.cif.gz | 83.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cuh.ent.gz | 61.3 KB | Display | PDB format |
PDBx/mmJSON format | 3cuh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3cuh_validation.pdf.gz | 752.2 KB | Display | wwPDB validaton report |
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Full document | 3cuh_full_validation.pdf.gz | 752.8 KB | Display | |
Data in XML | 3cuh_validation.xml.gz | 17 KB | Display | |
Data in CIF | 3cuh_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cuh ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cuh | HTTPS FTP |
-Related structure data
Related structure data | 3cufC 3cugC 3cuiC 3cujC 2exoS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 34267.148 Da / Num. of mol.: 1 / Fragment: sequence database residues 43-357 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulomonas fimi (bacteria) / Gene: cex / Plasmid: pUC12 / Production host: Escherichia coli (E. coli) References: UniProt: Q59277, UniProt: P07986*PLUS, cellulose 1,4-beta-cellobiosidase (non-reducing end) |
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#2: Chemical | ChemComp-G2I / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 29, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Osmic focussing optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.87→30 Å / Num. all: 25315 / Num. obs: 25315 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 21 % / Rmerge(I) obs: 0.05 / Χ2: 1.003 / Net I/σ(I): 22.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2EXO Resolution: 1.89→19.99 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.348 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.271 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→19.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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