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Yorodumi- PDB-1v0m: Xylanase Xyn10a from Streptomyces lividans in complex with xylobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v0m | |||||||||
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Title | Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 7.5 | |||||||||
Components | ENDO-1,4-BETA-XYLANASE A | |||||||||
Keywords | HYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLANASE / XYLAN DEGRADATION / DEOXYNOJIRIMYCIN | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | STREPTOMYCES LIVIDANS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | |||||||||
Authors | Gloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki, J. / Withers, S.G. / Davies, G.J. | |||||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2004 Title: Atomic Resolution Analyses of the Binding of Xylobiose-Derived Deoxynojirimycin and Isofagomine to Xylanase Xyn10A Authors: Gloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki, J. / Withers, S.G. / Davies, G.J. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v0m.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v0m.ent.gz | 119.9 KB | Display | PDB format |
PDBx/mmJSON format | 1v0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/1v0m ftp://data.pdbj.org/pub/pdb/validation_reports/v0/1v0m | HTTPS FTP |
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-Related structure data
Related structure data | 1v0kC 1v0lC 1v0nC 1od8S 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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Unit cell |
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-Components
#1: Protein | Mass: 34129.457 Da / Num. of mol.: 1 / Fragment: CATALYTIC MODULE, RESIDUES 42-354 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES LIVIDANS (bacteria) / Production host: STREPTOMYCES LIVIDANS (bacteria) / Strain (production host): IAF 19 / References: UniProt: P26514, endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-XDN / |
#3: Sugar | ChemComp-XYP / |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
Compound details | CONTRIBUTES TO THE HYDROLYSIS OF HEMICELLULOSE, WHICH IS THE MAJOR COMPONENT OF PLANT CELL-WALLS. ...CONTRIBUTE |
Sequence details | THE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND TO THE SIGNAL PEPTIDE. THE NUMBERING USED IN THE ...THE FIRST 41 RESIDUES IN THE DATABASE CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 36.5 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 7.5 Details: 100 MM IMIDAZOLE, PH 7.5 16% PEG 5K MME, 5% ISOPROPANOL |
-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 CCD / Detector: CCD / Date: Sep 15, 2002 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER |
Radiation | Monochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→20 Å / Num. obs: 117436 / % possible obs: 94.4 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.54 |
Reflection shell | Resolution: 1.07→1.11 Å / Redundancy: 5.93 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.94 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD8 Resolution: 1.07→19.65 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.98 / SU B: 0.627 / SU ML: 0.014 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS THE LAST 11 AMINO ACIDS ARE TOO DISORDERED TO BE BUILT IN DENSITY.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 7.7 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→19.65 Å
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Refine LS restraints |
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