+Open data
-Basic information
Entry | Database: PDB / ID: 1xyf | ||||||
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Title | ENDO-1,4-BETA-XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS | ||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||
Keywords | HYDROLASE / Xylan degradation | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Fujimoto, Z. / Mizuno, H. / Kuno, A. / Kusakabe, I. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain. Authors: Fujimoto, Z. / Kuno, A. / Kaneko, S. / Yoshida, S. / Kobayashi, H. / Kusakabe, I. / Mizuno, H. #1: Journal: J.Biochem.(Tokyo) / Year: 1997 Title: Crystallization and Preliminary X-Ray Crystallographic Study of Streptomyces olivaceoviridis E-86 Xylanase Authors: Fujimoto, Z. / Mizuno, H. / Kuno, A. / Yoshida, S. / Kobayashi, H. / Kusakabe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xyf.cif.gz | 179.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xyf.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xy/1xyf ftp://data.pdbj.org/pub/pdb/validation_reports/xy/1xyf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.424, -0.9053, 0.0249), Vector: |
-Components
#1: Protein | Mass: 46791.223 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, XYLAN-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Streptomyces olivaceoviridis (bacteria) / Strain: E-86 / 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: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58 % | |||||||||||||||||||||||||
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Crystal grow | pH: 5.7 Details: 25% SATURATED AMMONIUM SULFATE, 2% MCILVAINE BUFFER PH 5.7 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Date: Dec 1, 1994 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→100 Å / Num. obs: 80196 / % possible obs: 94.2 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.9→1.971 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 4.9 / % possible all: 77.7 |
Reflection | *PLUS Num. measured all: 441579 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1XAS, 2EXO Resolution: 1.9→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Lowest resolution: 1.97 Å / Rfactor Rfree: 0.353 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.304 / Rfactor obs: 0.305 |