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- PDB-1v0k: Xylanase Xyn10A from Streptomyces lividans in complex with xylobi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1v0k | |||||||||
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Title | Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-deoxynojirimycin at pH 5.8 | |||||||||
![]() | ENDO-1,4-BETA-XYLANASE A | |||||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE FAMILY 10 / XYLANASE / XYLAN DEGRADATION / DEOXYNOJIRIMYCIN | |||||||||
Function / homology | ![]() endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / carbohydrate binding / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Gloster, T.M. / Williams, S.J. / Roberts, S. / Tarling, C.A. / Wicki S, J. / Withers, G. / Davies, G.J. | |||||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 164.8 KB | Display | ![]() |
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PDB format | ![]() | 129 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
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Full document | ![]() | 463.9 KB | Display | |
Data in XML | ![]() | 21.7 KB | Display | |
Data in CIF | ![]() | 35.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1v0lC ![]() 1v0mC ![]() 1v0nC ![]() 1od8S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() |
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#2: Sugar | ChemComp-XYP / |
#3: Chemical | ChemComp-XDN / |
#4: 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: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.3 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
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Crystal grow | pH: 5.8 Details: 20 MG/ML PROTEIN, 0.1 M MES, PH 5.8, 18% PEG 5K MME, 7.5% ISOPROPANOL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2003 / 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: 1.03→30 Å / Num. obs: 128937 / % possible obs: 97.1 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.03→1.05 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.31 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OD8 Resolution: 1.03→27.15 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.712 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY A CIS-PEPTIDE BOND BETWEEN RESIDUES 89 AND 90 IS MANIFESTED ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 1 AND THE LAST 11 RESIDUES ARE TOO DISORDERED TO BE BUILT IN DENSITY A CIS-PEPTIDE BOND BETWEEN RESIDUES 89 AND 90 IS MANIFESTED BECAUSE THE MAIN CHAIN IS BUILT IN DOUBLE CONFORMATION.
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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: 7.54 Å2
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Refinement step | Cycle: LAST / Resolution: 1.03→27.15 Å
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Refine LS restraints |
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