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Yorodumi- PDB-3kl0: Crystal structure of the glucuronoxylan xylanohydrolase XynC from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kl0 | ||||||
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Title | Crystal structure of the glucuronoxylan xylanohydrolase XynC from Bacillus subtilis | ||||||
Components | Glucuronoxylanase xynC | ||||||
Keywords | HYDROLASE / alpha beta barrel / (beta/alpha)8 barrel (beta/alpha)8 + beta dual motif family | ||||||
Function / homology | Function and homology information glucuronoarabinoxylan endo-1,4-beta-xylanase / glucuronoarabinoxylan endo-1,4-beta-xylanase activity / glucosylceramidase activity / sphingolipid metabolic process / xylan catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 Å | ||||||
Authors | St John, F.J. / Hurlbert, J.C. / Pozharski, E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Ligand bound structures of a glycosyl hydrolase family 30 glucuronoxylan xylanohydrolase. Authors: St John, F.J. / Hurlbert, J.C. / Rice, J.D. / Preston, J.F. / Pozharski, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kl0.cif.gz | 375 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kl0.ent.gz | 302.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kl0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3kl0 ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3kl0 | HTTPS FTP |
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-Related structure data
Related structure data | 3kl3C 3kl5C 3gtnS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 45431.465 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: subspecies subtilis, strain 168 / Gene: BSU18150, xynC, ynfF / Plasmid: pET41xyncC-ter Octa His / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) References: UniProt: Q45070, glucuronoarabinoxylan endo-1,4-beta-xylanase |
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-Non-polymers , 5 types, 2200 molecules
#2: Chemical | ChemComp-MLA / #3: Chemical | ChemComp-TAR / | #4: Chemical | #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | AUTHOR BELIEVES THAT FLOATING DIPEPTIDE, HIS 405 A AND HIS 406 A, BELONGS TO C-TERMINUS OF SYMMETRY ...AUTHOR BELIEVES THAT FLOATING DIPEPTIDE, HIS 405 A AND HIS 406 A, BELONGS TO C-TERMINUS OF SYMMETRY RELATED CHAIN D WITH REST OF THE HIS TAGS DISORDERED |
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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: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 294.65 K / Method: vapor diffusion, sitting drop Details: 200 mM Na Tartrate 200 mM Na Malonate pH 7.0 19% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294.65K |
-Data collection
Diffraction | Mean temperature: 105 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97607 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97607 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→50 Å / Num. obs: 220570 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GTN Resolution: 1.64→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.828 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.664 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.64→1.681 Å / Total num. of bins used: 20
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