+Open data
-Basic information
Entry | Database: PDB / ID: 5gv1 | ||||||
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Title | Crystal structure of ENZbleach xylanase wild type | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / Endo-1 / 4-beta-xylanase / GH11 xylanase | ||||||
Biological species | termite gut metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å | ||||||
Model details | Crystal structure of ENZbleach xylanase wild type | ||||||
Authors | Chitnumsub, P. / Jaruwat, A. / Boonyapakorn, K. / Noytanom, K. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: J. Biotechnol. / Year: 2017 Title: Structure-based protein engineering for thermostable and alkaliphilic enhancement of endo-beta-1,4-xylanase for applications in pulp bleaching Authors: Boonyapakron, K. / Jaruwat, A. / Liwnaree, B. / Nimchua, T. / Champreda, V. / Chitnumsub, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gv1.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gv1.ent.gz | 54.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gv1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gv1 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gv1 | HTTPS FTP |
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-Related structure data
Related structure data | 5gy8C 5gy9C 5gyaC 5gybC 5gycC 5gyeC 5gyfC 5gygC 5gyhC 5gyiC 1ig0S S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 35842.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) termite gut metagenome (others) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: endo-1,4-beta-xylanase |
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#2: Water | ChemComp-HOH / |
Sequence details | Residues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the ...Residues (-35)-0 and 274-286 in the sample sequence are His-tag sequence. Residues 1-273 in the sample sequence is the xylanase protein. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.38 % / Mosaicity: 0.78 ° |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 6.5 / Details: PEG 1500, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 14, 2013 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: GRAPHITE / 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→30 Å / Num. obs: 38524 / % possible obs: 91 % / Redundancy: 2.27 % / Biso Wilson estimate: 10.184 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 11.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IG0 Resolution: 1.5→29.91 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.234 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.081 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 41.07 Å2 / Biso mean: 9.488 Å2 / Biso min: 4.81 Å2
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Refinement step | Cycle: final / Resolution: 1.5→29.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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