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Yorodumi- PDB-1uhv: Crystal structure of beta-D-xylosidase from Thermoanaerobacterium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1uhv | ||||||
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Title | Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase | ||||||
Components | Beta-xylosidase | ||||||
Keywords | HYDROLASE / family 39 glycoside hydrolase / xylosidase / xylan / xylose / covalent glycosyl-enzyme intermediate | ||||||
Function / homology | Function and homology information xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / xylan catabolic process Similarity search - Function | ||||||
Biological species | Thermoanaerobacterium saccharolyticum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Yang, J.K. / Yoon, H.J. / Ahn, H.J. / Il Lee, B. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. ...Yang, J.K. / Yoon, H.J. / Ahn, H.J. / Il Lee, B. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. / Vocadlo, D.J. / Withers, S.G. / Suh, S.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Crystal structure of beta-D-xylosidase from Thermoanaerobacterium saccharolyticum, a family 39 glycoside hydrolase. Authors: Yang, J.K. / Yoon, H.J. / Ahn, H.J. / Lee, B.I. / Pedelacq, J.D. / Liong, E.C. / Berendzen, J. / Laivenieks, M. / Vieille, C. / Zeikus, G.J. / Vocadlo, D.J. / Withers, S.G. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uhv.cif.gz | 434.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uhv.ent.gz | 356 KB | Display | PDB format |
PDBx/mmJSON format | 1uhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uhv_validation.pdf.gz | 487 KB | Display | wwPDB validaton report |
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Full document | 1uhv_full_validation.pdf.gz | 545.1 KB | Display | |
Data in XML | 1uhv_validation.xml.gz | 89.1 KB | Display | |
Data in CIF | 1uhv_validation.cif.gz | 125 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/1uhv ftp://data.pdbj.org/pub/pdb/validation_reports/uh/1uhv | HTTPS FTP |
-Related structure data
Related structure data | 1px8SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is the tetramer in a crystallographically asymmetric unit |
-Components
#1: Protein | Mass: 58739.180 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium saccharolyticum (bacteria) Plasmid: pXHP3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P36906, xylan 1,4-beta-xylosidase #2: Sugar | ChemComp-DFX / #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: 2.32 Å3/Da / Density % sol: 46.49 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 2000 MME, Tris-HCl, dithiothreitol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.9792 Å |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: May 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 125254 / Num. obs: 125254 / % possible obs: 92.2 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 6.5 Å2 / Rsym value: 0.074 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.14 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.211 / % possible all: 83.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PX8 Resolution: 2.1→32.33 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 798853.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.1467 Å2 / ksol: 0.336387 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→32.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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