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Yorodumi- PDB-2w5f: High resolution crystallographic structure of the Clostridium the... -
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-Basic information
Entry | Database: PDB / ID: 2w5f | |||||||||
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Title | High resolution crystallographic structure of the Clostridium thermocellum N-terminal endo-1,4-beta-D-xylanase 10B (Xyn10B) CBM22-1- GH10 modules complexed with xylohexaose | |||||||||
Components | ENDO-1,4-BETA-XYLANASE Y | |||||||||
Keywords | HYDROLASE / CELLULOSOME / 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 / SAD / Resolution: 1.9 Å | |||||||||
Authors | Najmudin, S. / Pinheiro, B.A. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. | |||||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Putting an N-Terminal End to the Clostridium Thermocellum Xylanase Xyn10B Story: Crystal Structure of the Cbm22-1-Gh10 Modules Complexed with Xylohexaose. Authors: Najmudin, S. / Pinheiro, B.A. / Prates, J.A.M. / Gilbert, H.J. / Romao, M.J. / Fontes, C.M.G.A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2008 Title: Purification, Crystallization and Crystallographic Analysis of Clostridium Thermocellum Endo-1,4-Beta- D-Xylanase 10B in Complex with Xylohexaose. Authors: Najmudin, S. / Pinheiro, B.A. / Romao, M.J. / Prates, J.A.M. / Fontes, C.M.G.A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w5f.cif.gz | 255 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w5f.ent.gz | 203.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w5f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w5f_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2w5f_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2w5f_validation.xml.gz | 56.3 KB | Display | |
Data in CIF | 2w5f_validation.cif.gz | 87.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w5f ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w5f | HTTPS FTP |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 60082.301 Da / Num. of mol.: 2 / Fragment: CBM22-1, RESIDUES 32-551 / Mutation: YES Source method: isolated from a genetically manipulated source Details: 2 XYLOHEXAOSES (BUT ONLY 3 OF THE 6 XYLOSE RINGS CAN BE SEEN IN THE ELECTRON DENSITY), 9 ACETATES, 13 CADMIUM IONS Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Strain: YS / Plasmid: PGEM T-EASY, PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL10-GOLD, BL21(DE3) / References: UniProt: P51584, endo-1,4-beta-xylanase #2: Polysaccharide | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CD / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Nonpolymer details | CELLOHEXAOSE (XYP): WE ONLY SEE THREE OF THE SIX XYLOSE UNITS FOR EACH OF THE XYLOHEXAOSES IN THE ...CELLOHEXAO | Sequence details | THE PROTEIN SEQUENCE OF THE CONSTRUCT CORRESPONDS TO AMINO ACID RESIDUES 32 TO 551 WITH THE E337A ...THE PROTEIN SEQUENCE OF THE CONSTRUCT CORRESPOND | |
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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: 4.74 Å3/Da / Density % sol: 74.07 % Description: THE PDB COORDINATES FOR 2W5F WERE SUBMITTED TO CAPRI. THE RESULTS OF THE LAST CAPRI ROUND ARE NOW AVAILABLE AT HTTP://WWW.EBI.AC.UK/MSD-SRV/CAPRI/ROUND15/ROUND15.HTML AS T35 AND T36 (WITH BOUND CBM22). |
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Crystal grow | Temperature: 292 K / pH: 7.5 Details: 1 M NA ACETATE, 0.1 M HEPES PH 7.5, 0.05 M CDSO4, 10 MM XYLOHEXAOSE AT 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2→65.8 Å / Num. obs: 176859 / % possible obs: 99.9 % / Observed criterion σ(I): 1.7 / Redundancy: 19.2 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.9→2.11 Å / Redundancy: 10.5 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.7 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.9→150.76 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.404 / SU ML: 0.083 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES A181-A190 AND B182-B189 ARE DISORDERED.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→150.76 Å
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Refine LS restraints |
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