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Open data
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Basic information
Entry | Database: PDB / ID: 2dep | ||||||
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Title | Crystal Structure of xylanase B from Clostridium stercorarium F9 | ||||||
![]() | Thermostable celloxylanase | ||||||
![]() | HYDROLASE / GLYCOSIDASE / XYLAN DEGRADATION / FAMILY 10 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses | ||||||
Function / homology | ![]() cellulase / endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / cellulase activity / xylan catabolic process / cellulose catabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Fushinobu, S. / Nishimoto, M. / Miyanaga, A. / Kitaoka, M. / Hayashi, K. | ||||||
![]() | ![]() Title: Molecular anatomy of the alkaliphilic xylanase from Bacillus halodurans C-125 Authors: Nishimoto, M. / Fushinobu, S. / Miyanaga, A. / Kitaoka, M. / Hayashi, K. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2004 Title: Crystallization and preliminary X-ray analysis of xylanase B from Clostridium stercorarium Authors: Nishimoto, M. / Fushinobu, S. / Miyanaga, A. / Wakagi, T. / Shoun, H. / Sakka, K. / Ohmiya, K. / Nirasawa, S. / Kitaoka, M. / Hayashi, K. #2: Journal: Biosci.Biotechnol.Biochem. / Year: 2005 Title: The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases Authors: Nishimoto, M. / Kitaoka, M. / Fushinobu, S. / Hayashi, K. #3: Journal: J.Biosci.Bioeng. / Year: 2002 Title: Employing chimeric xylanases to identify regions of an alkaline xylanase participating in enzyme activity at basic pH Authors: Nishimoto, M. / Kitaoka, M. / Hayashi, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 126.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.7 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 32.2 KB | Display | |
Data in CIF | ![]() | 49.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hizS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41365.602 Da / Num. of mol.: 2 / Fragment: residues 41-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P40942, cellulase, endo-1,4-beta-xylanase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 24% PEG 1500, 20% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 23, 2003 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50.14 Å / Num. all: 81152 / Num. obs: 80942 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.276 / Mean I/σ(I) obs: 2.5 / Num. unique all: 8015 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HIZ Resolution: 1.8→50.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2018982.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.5148 Å2 / ksol: 0.388148 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→50.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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