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Yorodumi- PDB-3m4f: Structural insights into the acidophilic pH adaptation of a novel... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3m4f | ||||||
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Title | Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase from Scytalidium acidophilum | ||||||
Components | Endo-1,4-beta-xylanaseXylanase | ||||||
Keywords | HYDROLASE / family 11 endoxylanase / acidophilic adaptation / structure/function relationship / Glycosidase / Xylan degradation | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process Similarity search - Function | ||||||
Biological species | Scytalidium acidophilum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Michaux, C. / Wouters, J. | ||||||
Citation | Journal: Biochimie / Year: 2010 Title: Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase from Scytalidium acidophilum Authors: Michaux, C. / Pouyez, J. / Mayard, A. / Vandurm, P. / Housen, I. / Wouters, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m4f.cif.gz | 162.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m4f.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 3m4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m4/3m4f ftp://data.pdbj.org/pub/pdb/validation_reports/m4/3m4f | HTTPS FTP |
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-Related structure data
Related structure data | 1bk1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21816.295 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Scytalidium acidophilum (fungus) / Gene: Xyl1 / Production host: Pichia pastoris (fungus) / References: UniProt: Q6VAY1, endo-1,4-beta-xylanase #2: Chemical | ChemComp-CXS / #3: 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: 2.89 Å3/Da / Density % sol: 57.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5 Details: 2M ammonium sulphate, 100mM CAPS (pH 10.5) and 200mM sulphate lithium, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→20 Å / Num. obs: 80178 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 1.89→2 Å / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 9.49 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK1 Resolution: 1.89→5.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.44 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.348 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.89→5.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.934 Å / Total num. of bins used: 20
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