+Open data
-Basic information
Entry | Database: PDB / ID: 4xqd | |||||||||
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Title | X-ray structure analysis of xylanase-WT at pH4.0 | |||||||||
Components | Endo-1,4-beta-xylanase 2Xylanase | |||||||||
Keywords | HYDROLASE / jelly roll | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Wan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. ...Wan, Q. / Park, J.M. / Riccardi, D.M. / Hanson, L.B. / Fisher, Z. / Smith, J.C. / Ostermann, A. / Schrader, T. / Graham, D.E. / Coates, L. / Langan, P. / Kovalevsky, A.Y. | |||||||||
Funding support | United States, China, 2items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / 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. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Preliminary joint X-ray and neutron protein crystallographic studies of endoxylanase II from the fungus Trichoderma longibrachiatum. Authors: Kovalevsky, A.Y. / Hanson, B.L. / Seaver, S. / Fisher, S.Z. / Mustyakimov, M. / Langan, P. #2: Journal: Acta Crystallogr.,Sect.D / 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. #3: Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Heterologous expression, purification, crystallization and preliminary X-ray analysis of Trichoderma reesei xylanase II and four variants. Authors: Wan, Q. / Kovalevsky, A. / Zhang, Q. / Hamilton-Brehm, S. / Upton, R. / Weiss, K.L. / Mustyakimov, M. / Graham, D. / Coates, L. / Langan, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xqd.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xqd.ent.gz | 73.2 KB | Display | PDB format |
PDBx/mmJSON format | 4xqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/4xqd ftp://data.pdbj.org/pub/pdb/validation_reports/xq/4xqd | HTTPS FTP |
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-Related structure data
Related structure data | 4s2dC 4s2fC 4s2gC 4s2hC 4xpvC 4xq4C 4xqwC 2dfbS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | biological unit is the same as asym. |
-Components
#1: Protein | Mass: 20727.338 Da / Num. of mol.: 2 / Fragment: substrate-binding groove, jelly roll Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea jecorina (fungus) / Gene: xyn2 / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold / References: UniProt: P36217, endo-1,4-beta-xylanase #2: Chemical | ChemComp-IOD / #3: Chemical | ChemComp-TRS / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.76 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 20% PEG8000, 0.2 M NaI, 0.1 M NaOAc at pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 12, 2013 / Details: Mirrors |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. obs: 56145 / % possible obs: 91.2 % / Redundancy: 2.3 % / Rsym value: 0.098 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.1 / % possible all: 88.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DFB Resolution: 1.5→19.956 Å / FOM work R set: 0.8158 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.38 / 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: 48.7 Å2 / Biso mean: 19.67 Å2 / Biso min: 3.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→19.956 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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