+Open data
-Basic information
Entry | Database: PDB / ID: 5zo0 | ||||||
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Title | Neutron structure of xylanase at pD5.4 | ||||||
Components | Endo-1,4-beta-xylanase 2Xylanase | ||||||
Keywords | HYDROLASE / family 11 GH / neutron crystallography / protonation state | ||||||
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 | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.648 Å | ||||||
Authors | Wan, Q. / Li, Z.H. | ||||||
Funding support | China, 1items
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Citation | #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 | 5zo0.cif.gz | 95.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zo0.ent.gz | 74.1 KB | Display | PDB format |
PDBx/mmJSON format | 5zo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/5zo0 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/5zo0 | HTTPS FTP |
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-Related structure data
Related structure data | 2dfcS S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.1073/pnas.1504986112 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20727.338 Da / Num. of mol.: 1 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 / Plasmid: pET-NTMST / Details (production host): pET-28(b) derivative / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM (DE3) / References: UniProt: P36217, endo-1,4-beta-xylanase |
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#2: Chemical | ChemComp-DOD / |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 295 K Details: The crystal was then sealed in a capillary with the D2O exchanged solution (2% PEG 3350, 0.2M NaI, 0.1M NaAc, pD5.4) for pH equilibration for two weeks before data collection (pD = pH + 0.4) Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M Tris, 0.1M NaCl, 1mM DTT, pH8.0, 2% PEG 3350, 0.2M NaI Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 295 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: NUCLEAR REACTOR / Site: FRM II / Beamline: BIODIFF / Wavelength: 2.66 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: BIODIFF / Detector: IMAGE PLATE / Date: Oct 1, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: pyrolytic graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 2.66 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 22574 / % possible obs: 86.1 % / Redundancy: 2 % / Biso Wilson estimate: 7.29 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.103 / Rrim(I) all: 0.17 / Χ2: 0.991 / Net I/σ(I): 7.1 / Num. measured all: 44926 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dfc Resolution: 1.648→22.864 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.15 Å2 / Biso mean: 21.9251 Å2 / Biso min: 3.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→22.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: NEUTRON DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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