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Yorodumi- PDB-1wb5: S954A mutant of the feruloyl esterase module from clostridium the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wb5 | ||||||
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Title | S954A mutant of the feruloyl esterase module from clostridium thermocellum complexed with syringate | ||||||
Components | ENDO-1,4-BETA-XYLANASE Y | ||||||
Keywords | HYDROLASE / ESTERASE FAMILY 1 / FERULIC ACID / GLYCOSIDASE / XYLAN DEGRADATION / XYLANASE | ||||||
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 | 1wb5.cif.gz | 272.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1wb5.ent.gz | 218.7 KB | Display | PDB format |
PDBx/mmJSON format | 1wb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/1wb5 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/1wb5 | HTTPS FTP |
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-Related structure data
Related structure data | 1wb4C 1wb6C 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) / Plasmid: PET22B / 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, 684 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. THE SEQUENCE CONFLICTS (RESIDUES ...ONLY THE FERULOYL ESTERASE DOMAIN WAS SUBCLONED. S954A MUTANT. THE SEQUENCE CONFLICTS (RESIDUES 1017 AND 1018) ARE DUE TO ERRORS IN THE UNIPROT ENTRY FROM THE ORIGINAL SEQUENCING |
-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: NA ACETATE 1M HEPES PH 7.5 100MM CD ACETATE 50MM GLYCEROL 5% |
-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 13, 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: 158021 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.4 / % possible all: 90.6 |
-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: 0.979 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.517 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.041 / 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: 10.95 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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