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Yorodumi- PDB-7kn8: Crystal structure of the GH74 xyloglucanase from Xanthomonas camp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kn8 | |||||||||||||||
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Title | Crystal structure of the GH74 xyloglucanase from Xanthomonas campestris (Xcc1752) | |||||||||||||||
Components | Cellulase | |||||||||||||||
Keywords | HYDROLASE / Glycoside Hydrolase Family 74 / Xyloglucanase / Xyloglucan | |||||||||||||||
Function / homology | xyloglucan metabolic process / WD40/YVTN repeat-like-containing domain superfamily / IODIDE ION / Cellulase Function and homology information | |||||||||||||||
Biological species | Xanthomonas campestris pv. campestris (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||||||||
Authors | Araujo, E.A. / Vieira, P.S. / Murakami, M.T. / Polikarpov, I. | |||||||||||||||
Funding support | Brazil, 4items
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Citation | Journal: Nature Communications / Year: 2021 Title: Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, ...Authors: Vieira, P.S. / Bonfim, I.M. / Araujo, E.A. / Melo, R.R. / Lima, A.R. / Fessel, M.R. / Paixao, D.A.A. / Persinoti, G.F. / Rocco, S.A. / Lima, T.B. / Pirolla, R.A.S. / Morais, M.A.B. / Correa, J.B.L. / Zanphorlin, L.M. / Diogo, J.A. / Lima, E.A. / Grandis, A. / Buckeridge, M.S. / Gozzo, F.C. / Benedetti, C.E. / Polikarpov, I. / Giuseppe, P.O. / Murakami, M.T. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7kn8.cif.gz | 541 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kn8.ent.gz | 440.3 KB | Display | PDB format |
PDBx/mmJSON format | 7kn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kn8_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7kn8_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7kn8_validation.xml.gz | 58.2 KB | Display | |
Data in CIF | 7kn8_validation.cif.gz | 88.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/7kn8 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/7kn8 | HTTPS FTP |
-Related structure data
Related structure data | 7kmmC 7kmnC 7kmoC 7kmpC 7kmqC 7kncC 2cn2S 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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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 77306.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris pv. campestris (strain ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25) (bacteria) Strain: ATCC 33913 / DSM 3586 / NCPPB 528 / LMG 568 / P 25 / Gene: XCC1752 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8P9U5 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 1109 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | ChemComp-IOD / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.23 Å3/Da / Density % sol: 44.97 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 mol/L sodium iodede 0.1 mol/L bis-tris propane 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45855 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2012 |
Radiation | Monochromator: Water-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45855 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.992 Å / Num. obs: 99662 / % possible obs: 98.1 % / Redundancy: 12.191 % / CC1/2: 0.997 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 1.95→2.07 Å / Redundancy: 10.12 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 15178 / CC1/2: 0.888 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CN2 Resolution: 1.95→19.992 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 64.54 Å2 / Biso mean: 19.4244 Å2 / Biso min: 14.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.95→19.992 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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