[English] 日本語
Yorodumi- PDB-1v0n: Xylanase Xyn10a from Streptomyces lividans in complex with xylobi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v0n | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-isofagomine 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: 1.1 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 |
| |||||||||
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 |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1v0n.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1v0n.ent.gz | 123.6 KB | Display | PDB format |
PDBx/mmJSON format | 1v0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v0n_validation.pdf.gz | 469.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1v0n_full_validation.pdf.gz | 469.9 KB | Display | |
Data in XML | 1v0n_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 1v0n_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v0/1v0n ftp://data.pdbj.org/pub/pdb/validation_reports/v0/1v0n | HTTPS FTP |
-Related structure data
Related structure data | 1v0kC 1v0lC 1v0mC 1od8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 2 molecules A
#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 |
---|---|
#4: Sugar | ChemComp-XYP / |
-Non-polymers , 4 types, 622 molecules
#2: Chemical | #3: Chemical | ChemComp-XIF / | #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
---|
-Details
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 |
---|
-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 36.5 % / Description: STRUCTURE ISOMORPHOUS WITH STARTING MODEL |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.025 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 15, 2003 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL, SI(111) OR SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.025 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→23 Å / Num. obs: 97030 / % possible obs: 95.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.1→1.16 Å / Redundancy: 3 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.6 / % possible all: 70.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OD8 Resolution: 1.1→22.85 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.982 / SU B: 0.659 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 8.29 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→22.85 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|