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Yorodumi- PDB-5zii: Crystal Structures of Mutant Endo-beta-1,4-xylanase II (Y88F)Comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zii | |||||||||
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Title | Crystal Structures of Mutant Endo-beta-1,4-xylanase II (Y88F)Complexed with Xylotriose | |||||||||
Components | Endo-1,4-beta-xylanase 2 | |||||||||
Keywords | HYDROLASE / Mutant Xylanase Complexed with Xylotriose | |||||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | |||||||||
Biological species | Hypocrea jecorina (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | |||||||||
Authors | Zhang, X. / Wan, Q. | |||||||||
Funding support | China, 1items
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Citation | Journal: to be published Title: Crystal Structures of Endo-beta-1,4-xylanase II Authors: Wan, Q. / Zhang, X. #1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2015 Title: Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Authors: Wan, Q. / Parks, J.M. / Hanson, B.L. / Fisher, S.Z. / Ostermann, A. / Schrader, T.E. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A. #2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2014 Title: X-ray crystallographic studies of family 11 xylanase Michaelis and product complexes: implications for the catalytic mechanism. Authors: Wan, Q. / Zhang, Q. / Hamilton-Brehm, S. / Weiss, K. / Mustyakimov, M. / Coates, L. / Langan, P. / Graham, D. / Kovalevsky, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zii.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zii.ent.gz | 97.8 KB | Display | PDB format |
PDBx/mmJSON format | 5zii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zii_validation.pdf.gz | 727.6 KB | Display | wwPDB validaton report |
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Full document | 5zii_full_validation.pdf.gz | 728.7 KB | Display | |
Data in XML | 5zii_validation.xml.gz | 12 KB | Display | |
Data in CIF | 5zii_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5zii ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5zii | HTTPS FTP |
-Related structure data
Related structure data | 5zh0C 5ziwC 5zkzC 2dfcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.1107/S1399004713023626 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20711.338 Da / Num. of mol.: 1 / Mutation: Y88F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30) (fungus) Strain: ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30 / Gene: xyn2, M419DRAFT_124931 / Production host: Escherichia coli (E. coli) / References: UniProt: P36217, endo-1,4-beta-xylanase | ||
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#2: Polysaccharide | beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose / 4beta-beta-xylotriose | ||
#3: Chemical | ChemComp-IOD / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.77 % |
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Crystal grow | Temperature: 291 K / Method: evaporation / pH: 6 / Details: 20% PEG 8000, 0.2M NaI, 0.1M MES |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→29.911 Å / Num. obs: 47482 / % possible obs: 94.58 % / Redundancy: 6.5 % / Biso Wilson estimate: 13.43 Å2 / Rmerge(I) obs: 0.0222 / Net I/σ(I): 27.26 |
Reflection shell | Resolution: 1.3→1.346 Å / Redundancy: 6 % / Rmerge(I) obs: 0.1087 / Mean I/σ(I) obs: 6.1 / Num. unique obs: 4724 / % possible all: 96.66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DFC Resolution: 1.3→29.911 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 13.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.07 Å2 / Biso mean: 18.3403 Å2 / Biso min: 8.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→29.911 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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