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Yorodumi- PDB-6fj4: Structure of FAE solved by SAD from data collected at the peak of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fj4 | ||||||
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Title | Structure of FAE solved by SAD from data collected at the peak of the Selenium absorption edge on ID30B | ||||||
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 | Clostridium thermocellum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | McCarthy, A.A. / Mueller-Dieckmann, C. | ||||||
Citation | Journal: J Synchrotron Radiat / Year: 2018 Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fj4.cif.gz | 75.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fj4.ent.gz | 58.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fj4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/6fj4 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/6fj4 | HTTPS FTP |
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-Related structure data
Related structure data | 6fidC 6fj2C 6fj6C 6fj8C 6fj9C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/543 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32757.076 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium thermocellum (bacteria) / Gene: xynY / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P51584, endo-1,4-beta-xylanase | ||||||
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#2: Chemical | ChemComp-CD / #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 3.16 Å3/Da / Density % sol: 61.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES, 50 mM CdSO4, 5% (v/v) glycerol, and 1 M Na-acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 5, 2017 Details: Be CRL (vertical) and Rh Elliptical mirror (horizontal) |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→79.21 Å / Num. obs: 46013 / % possible obs: 96.3 % / Redundancy: 2.4 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.041 / Rrim(I) all: 0.091 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 1.39 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2462 / CC1/2: 0.318 / Rpim(I) all: 0.84 / Rrim(I) all: 1.83 / % possible all: 96.1 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 1.7→79.21 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.498 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.075 / 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: 1.3 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.906 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→79.21 Å
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