+Open data
-Basic information
Entry | Database: PDB / ID: 2a8z | ||||||
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Title | Structure Of A Cold-Adapted Family 8 Xylanase | ||||||
Components | endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / XYLAN DEGRADATION / PSYCHROPHILIC / COLD ADAPTATION / TEMPERATURE / GLYCOSYL HYDROLASE / FAMILY 8 | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudoalteromonas haloplanktis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Collins, T. / De Vos, D. / Hoyoux, A. / Savvides, S.N. / Gerday, C. / Van Beeumen, J. / Feller, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Study of the active site residues of a glycoside hydrolase family 8 xylanase. Authors: Collins, T. / De Vos, D. / Hoyoux, A. / Savvides, S.N. / Gerday, C. / Van Beeumen, J. / Feller, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a8z.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a8z.ent.gz | 69.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/2a8z ftp://data.pdbj.org/pub/pdb/validation_reports/a8/2a8z | HTTPS FTP |
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-Related structure data
Related structure data | 1xw2C 1xwqC 1xwtC 1h13S 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: 45980.758 Da / Num. of mol.: 1 / Mutation: D144A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas haloplanktis (bacteria) Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8RJN8, endo-1,4-beta-xylanase |
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#2: 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: 2.8 Å3/Da / Density % sol: 56.4 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: PEG8000, sodium cacodylate, ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8034 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 3, 2005 |
Radiation | Monochromator: - Triangular mono chromator - Bent mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8034 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→12 Å / Num. all: 8932 / Num. obs: 8337 / % possible obs: 93.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 3.2→3.27 Å / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 1H13 Resolution: 3.2→12 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.832 / SU B: 22.902 / SU ML: 0.409 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.588 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.668 Å2
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Refinement step | Cycle: LAST / Resolution: 3.2→12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.201→3.278 Å / Total num. of bins used: 20 /
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