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Yorodumi- PDB-1wb6: S954A mutant of the feruloyl esterase module from clostridium the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wb6 | ||||||
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Title | S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with vanillate | ||||||
Components | ENDO-1,4-BETA-XYLANASE Y | ||||||
Keywords | HYDROLASE / ESTERASE FAMILY 1 / FERULIC ACID / GLYCOSIDASE / XYLAN DEGRADATION | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Tarbouriech, N. / Prates, J.A. / Fontes, C. / Davies, G.J. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Molecular Determinants of Substrate Specificity in the Feruloyl Esterase Module of Xylanase 10B from Clostridium Thermocellum Authors: Tarbouriech, N. / Prates, J.A. / Fontes, C. / 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 | 1wb6.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wb6.ent.gz | 224.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wb6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/1wb6 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wb6 | HTTPS FTP |
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-Related structure data
Related structure data | 1wb4C 1wb5C 1gklS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 33748.539 Da / Num. of mol.: 2 / Fragment: FERULOYL ESTERASE DOMAIN, RESIDUES 792-1077 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P51584, endo-1,4-beta-xylanase |
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-Non-polymers , 5 types, 717 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Chemical | ChemComp-CD / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED MUTATION IN CHAIN A, SER 954 TO ALA ENGINEERED MUTATION IN CHAIN B, SER 954 TO ALA ...ENGINEERED |
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Sequence details | ONLY THE FERULOYL ESTERASE DOMAIN WAS SUBCLONED. S954A MUTANT |
-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: 1M NA ACETATE 100MM HEPES PH 7.5, 50MM CD ACETATE, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 12, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→80 Å / Num. obs: 157680 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.1 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GKL Resolution: 1.4→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.53 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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