+Open data
-Basic information
Entry | Database: PDB / ID: 2g4f | ||||||
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Title | Structure of S.olivaceoviridis xylanase Q88A/R275A mutant | ||||||
Components | Hydrolase | ||||||
Keywords | HYDROLASE / glycoside hydrolase | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Streptomyces olivaceoviridis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.65 Å | ||||||
Authors | Diertavitian, S. / Kaneko, S. / Fujimoto, Z. / Kuno, A. / Johansson, E. / Lo Leggio, L. | ||||||
Citation | Journal: PROCESS BIOCHEM / Year: 2012 Title: Structure-based engineering of glucose specificity in a family 10 xylanase from Streptomyces olivaceoviridis E-86 Authors: Ichinose, H. / Diertavitian, S. / Fujimoto, Z. / Kuno, A. / Leggio, L.L. / Kaneko, S. #1: Journal: Biotechnology of lignocellulose degradation and Biomass Utilization Year: 2004 Title: Structure and specificity of polysaccharidases belonging to Clan GH-A Authors: Lo Leggio, L. / Le Nours, J. / Ryttersgaard, C. / Kaneko, S. / Kuno, A. / Fujimoto, Z. / Diertavitian, S. / Larsen, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2g4f.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2g4f.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 2g4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/2g4f ftp://data.pdbj.org/pub/pdb/validation_reports/g4/2g4f | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
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Details | biological assembly is monomer, there are 2 biological units in the asymmetric unit. |
-Components
#1: Protein | Mass: 34034.383 Da / Num. of mol.: 2 / Fragment: catalytic domain, residues 1-302 / Mutation: Q88A/R275A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces olivaceoviridis (bacteria) Strain: E-86 / Plasmid: pET28a (Novagen) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q7SI98, endo-1,4-beta-xylanase #2: 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: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 0.1M ammonium sulphate, 0.2M sodium acetate buffer, 9% PEG 8000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.088 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 26, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.088 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→30 Å / Num. obs: 19121 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rsym value: 0.159 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.65→2.71 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.501 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.65→15 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.873 / SU B: 10.454 / SU ML: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.339 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.568 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4307 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.65→2.717 Å / Total num. of bins used: 20
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