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Yorodumi- PDB-7kmo: Crystal structure of the GH35 beta-galactosidase (Xac1772) from X... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kmo | |||||||||
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Title | Crystal structure of the GH35 beta-galactosidase (Xac1772) from Xanthomonas citri in complex with galactose | |||||||||
Components | Beta-galactosidase, GH35 | |||||||||
Keywords | HYDROLASE / Glycoside Hydrolase Family 35 / Xyloglucan | |||||||||
Function / homology | Function and homology information beta-galactosidase complex / beta-galactosidase activity / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | Xanthomonas axonopodis pv. citri (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.753 Å | |||||||||
Authors | Vieira, P.S. / Murakami, M.T. | |||||||||
Funding support | Brazil, 2items
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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 | 7kmo.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kmo.ent.gz | 97.4 KB | Display | PDB format |
PDBx/mmJSON format | 7kmo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kmo_validation.pdf.gz | 814 KB | Display | wwPDB validaton report |
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Full document | 7kmo_full_validation.pdf.gz | 818.1 KB | Display | |
Data in XML | 7kmo_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 7kmo_validation.cif.gz | 38.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/7kmo ftp://data.pdbj.org/pub/pdb/validation_reports/km/7kmo | HTTPS FTP |
-Related structure data
Related structure data | 7kmmC 7kmnC 7kmpC 7kmqC 7kn8C 7kncC 4d1iS 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: 59644.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas axonopodis pv. citri (strain 306) (bacteria) Strain: 306 / Gene: XAC1772 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PLM3 | ||||||||
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#2: Chemical | #3: Sugar | ChemComp-GLA / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.2 mol/L ammonium sulfate 8% glycerol 0.1 mmol/L tris |
-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: 1.45872 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2018 |
Radiation | Monochromator: Water-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.45872 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→19.447 Å / Num. obs: 63855 / % possible obs: 97.4 % / Redundancy: 6.47 % / CC1/2: 0.998 / Net I/σ(I): 8.92 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 5.958 % / Mean I/σ(I) obs: 0.64 / Num. unique obs: 10477 / CC1/2: 0.327 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4D1I Resolution: 1.753→19.447 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97 / 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: 113.91 Å2 / Biso mean: 37.8966 Å2 / Biso min: 23.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.753→19.447 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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