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Yorodumi- PDB-5fxm: Structure of FAE solved by SAD from data collected by Direct Data... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fxm | ||||||
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Title | Structure of FAE solved by SAD from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer | ||||||
Components | ENDO-1,4-BETA-XYLANASE Y | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information cellulosome / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | RUMINICLOSTRIDIUM THERMOCELLUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å | ||||||
Authors | Bowler, M.W. / Nurizzo, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Robodiff: Combining a Sample Changer and Goniometer for Highly Automated Macromolecular Crystallography Experiments. Authors: Nurizzo, D. / Bowler, M.W. / Caserotto, H. / Dobias, F. / Giraud, T. / Surr, J. / Guichard, N. / Papp, G. / Guijarro, M. / Mueller-Dieckmann, C. / Flot, D. / Mcsweeney, S. / Cipriani, F. / ...Authors: Nurizzo, D. / Bowler, M.W. / Caserotto, H. / Dobias, F. / Giraud, T. / Surr, J. / Guichard, N. / Papp, G. / Guijarro, M. / Mueller-Dieckmann, C. / Flot, D. / Mcsweeney, S. / Cipriani, F. / Theveneau, P. / Leonard, G.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fxm.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxm.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 5fxm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxm ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34266.562 Da / Num. of mol.: 1 / Fragment: RESIDUES 792-1077 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RUMINICLOSTRIDIUM THERMOCELLUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P51584, feruloyl esterase | ||
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#2: Chemical | ChemComp-CD / #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: 3.02 Å3/Da / Density % sol: 59.27 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 26, 2016 / Details: BE CRL |
Radiation | Monochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→49.9 Å / Num. obs: 32088 / % possible obs: 98.3 % / Observed criterion σ(I): 3 / Redundancy: 24.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.1 / % possible all: 83.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.99→79.18 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.862 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.009 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→79.18 Å
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Refine LS restraints |
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