+Open data
-Basic information
Entry | Database: PDB / ID: 5byw | ||||||
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Title | Crystal structure of engineered trifunctional CtCEL5E | ||||||
Components | Endoglucanase H | ||||||
Keywords | HYDROLASE / Ctcel5E / cellulose | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Model details | biofunctional cellulase/xylanase | ||||||
Authors | Lin, W.L. / Liang, P.H. / Ho, M.C. | ||||||
Citation | Journal: to be published Title: Crystal structure of engineered trifunctional CtCel5E Authors: Lin, W.L. / Liang, P.H. / Ho, M.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5byw.cif.gz | 334.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5byw.ent.gz | 272.7 KB | Display | PDB format |
PDBx/mmJSON format | 5byw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/5byw ftp://data.pdbj.org/pub/pdb/validation_reports/by/5byw | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 47372.660 Da / Num. of mol.: 5 / Fragment: UNP residues 290-654 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria) Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372 Gene: celH, Cthe_1472 / Plasmid: pHTPP13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16218, cellulase #2: Water | ChemComp-HOH / | |
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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: 3.13 Å3/Da / Density % sol: 60.71 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 50mM sodium acetate, 8% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Type: OTHER / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 4, 2014 |
Diffraction measurement | Details: 0.20 degrees, 6.2 sec, detector distance 350.00 mm / Method: \w scans |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Av R equivalents: 0.111 / Number: 1371705 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 92695 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.8 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.029 / Rrim(I) all: 0.115 / Rsym value: 0.111 / Χ2: 1.039 / Net I/av σ(I): 24.531 / Net I/σ(I): 9.8 / Num. measured all: 1371705 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 3.952 / Rsym value: 0.826 / % possible all: 100 |
Cell measurement | Reflection used: 1371705 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.269 / 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: 49.732 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
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Refine LS restraints |
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