+Open data
-Basic information
Entry | Database: PDB / ID: 1hiz | ||||||
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Title | Xylanase T6 (Xt6) from Bacillus Stearothermophilus | ||||||
Components | ENDO-1,4-BETA-XYLANASEXylanase | ||||||
Keywords | GLYCOSIDASE / XYLAN DEGRADATION / FAMILY 10 / THERMOPHILE | ||||||
Function / homology | Function and homology information endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | BACILLUS STEAROTHERMOPHILUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Sainz, G. / Tepplitsky, A. / Stojanoff, V. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Structure Determination of the Extracellular Xylanase from Geobacillus Stearothermophilus by Selenomethionyl MAD Phasing Authors: Teplitsky, A. / Mechaly, A. / Stojanoff, V. / Sainz, G. / Golan, G. / Feinberg, H. / Gilboa, R. / Reiland, V. / Zolotnitsky, G. / Shallom, D. / Thompson, A. / Shoham, Y. / Shoham, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hiz.cif.gz | 105 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hiz.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 1hiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hiz ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hiz | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43872.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Strain: NCIMB40221 / Cell: BACTERIA / Cellular location: EXTRA CELLULAR / Gene: XYNA / Cell (production host): BACTERIA / Cellular location (production host): EXTRACELLULAR / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40943, endo-1,4-beta-xylanase |
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#2: Sugar | ChemComp-GLA / |
#3: Sugar | ChemComp-GLC / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Compound details | ENDOHYDROL |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.14 Å3/Da / Density % sol: 75.86 % | ||||||||||||||||||||
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Crystal grow | pH: 5 Details: RESERVOIR: 1.5 M AMMONIUM SULFATE. 8% (W/V) MPD, pH 5.00 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: Teplitsky, A., (1997) Acta Cryst., D53, 608. | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88,0.9791,0.97 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 15, 1999 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→25 Å / Num. obs: 35080 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 12.2 | ||||||||||||
Reflection shell | Resolution: 2.4→2.45 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.212 / % possible all: 85 | ||||||||||||
Reflection | *PLUS Highest resolution: 2.4 Å / Num. obs: 35642 / % possible obs: 99.8 % / Redundancy: 4.5 % / Num. measured all: 161549 / Rmerge(I) obs: 0.055 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.4 Å / % possible obs: 100 % / Rmerge(I) obs: 0.211 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→24.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2184699.83 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.375956 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→24.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 25 Å / Rfactor obs: 0.156 / Rfactor Rfree: 0.186 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.188 |