+Open data
-Basic information
Entry | Database: PDB / ID: 3vsv | |||||||||
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Title | The complex structure of XylC with xylose | |||||||||
Components | Xylosidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / beta-xylosidase / product inhibition | |||||||||
Function / homology | Function and homology information : / Glycoside hydrolase 120, insertion domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor ...: / Glycoside hydrolase 120, insertion domain / Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Immunoglobulin-like / Sandwich / Mainly Beta Similarity search - Domain/homology | |||||||||
Biological species | Thermoanaerobacterium (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å | |||||||||
Authors | Huang, C.H. / Sun, Y. / Ko, T.P. / Ma, Y. / Chen, C.C. / Zheng, Y. / Chan, H.C. / Pang, X. / Wiegel, J. / Shao, W. / Guo, R.T. | |||||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: The substrate/product-binding modes of a novel GH120 beta-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485 Authors: Huang, C.H. / Sun, Y. / Ko, T.P. / Chen, C.C. / Zheng, Y. / Chan, H.C. / Pang, X. / Wiegel, J. / Shao, W. / Guo, R.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vsv.cif.gz | 597.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vsv.ent.gz | 486.8 KB | Display | PDB format |
PDBx/mmJSON format | 3vsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/3vsv ftp://data.pdbj.org/pub/pdb/validation_reports/vs/3vsv | HTTPS FTP |
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-Related structure data
Related structure data | 3vstSC 3vsuC 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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-Components
#1: Protein | Mass: 72845.398 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoanaerobacterium (bacteria) / Strain: JW/SL YS485 / Plasmid: pHsh / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: A2ICH1, xylan 1,4-beta-xylosidase #2: Sugar | ChemComp-XYP / #3: Sugar | ChemComp-XYS / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M sodium citrate, 15-17%(w/v) polyethylene glycol 3350, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Date: Mar 10, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→25 Å / Num. obs: 574432 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 1.48→1.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.3 / Num. unique all: 57397 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VST Resolution: 1.48→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.48→25 Å
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LS refinement shell | Resolution: 1.48→1.53 Å
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