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Yorodumi- PDB-3cui: Cellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cui | |||||||||
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Title | Cellulomonas fimi Xylanase/Cellulase Cex (Cf Xyn10A) in complex with sulfur substituted beta-1,4 xylotetraose | |||||||||
Components | Exo-beta-1,4-glucanase | |||||||||
Keywords | HYDROLASE / CEX / XYLANASE / Isofagomine inhibitor / TIM BARREL / CELLULOSE DEGRADATION / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 | 3cui.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cui.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 3cui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cu/3cui ftp://data.pdbj.org/pub/pdb/validation_reports/cu/3cui | HTTPS FTP |
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-Related structure data
Related structure data | 3cufC 3cugC 3cuhC 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: Polysaccharide | beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio- ...beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose-(1-4)-4-thio-beta-D-xylopyranose / thio-xylotetraose |
#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: 2.12 Å3/Da / Density % sol: 41.87 % |
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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: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2003 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.4→30 Å / Num. all: 58181 / Num. obs: 58006 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.6 % / Rmerge(I) obs: 0.129 / Χ2: 3.503 / Net I/σ(I): 15.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5→19.87 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.091 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.066 / 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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.368 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.538 Å / Total num. of bins used: 20
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