+Open data
-Basic information
Entry | Database: PDB / ID: 1gkk | ||||||
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Title | Feruloyl esterase domain of XynY from clostridium thermocellum | ||||||
Components | ENDO-1,4-BETA-XYLANASE Y | ||||||
Keywords | HYDROLASE / FERULIC ACID / ESTERASE FAMILY 1 | ||||||
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 / MAD / Resolution: 1.6 Å | ||||||
Authors | Prates, J.A.M. / Tarbouriech, N. / Charnock, S.J. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Davies, G.J. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The Structure of the Feruloyl Esterase Module of Xylanase 10B from Clostridium Thermocellum Provides Insights Into Substrate Recognition Authors: Prates, J.A.M. / Tarbouriech, N. / Charnock, S.J. / Fontes, C.M.G.A. / Ferreira, L.M.A. / Davies, G.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gkk.cif.gz | 143.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkk.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 1gkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkk ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34266.562 Da / Num. of mol.: 2 / Fragment: FERULOYL ESTERASE DOMAIN RESIDUES 792-1077 Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51584, endo-1,4-beta-xylanase #2: Chemical | ChemComp-CD / #3: Chemical | ChemComp-GOL / | #4: 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: 2.95 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: HEPES PH 7.5 100MM, NA ACETATE 1M, CD ACETATE 50 MM, GLYCEROL 5% | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9754,0.9796 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2000 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR | |||||||||
Radiation | Monochromator: SI / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→30 Å / Num. obs: 106584 / % possible obs: 99.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15 | |||||||||
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 3 / % possible all: 95.1 | |||||||||
Reflection | *PLUS Lowest resolution: 30 Å | |||||||||
Reflection shell | *PLUS % possible obs: 95.1 % / Mean I/σ(I) obs: 4.9 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.489 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.065 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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