+Open data
-Basic information
Entry | Database: PDB / ID: 7xgv | ||||||
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Title | Legionella glucosyltransferase | ||||||
Components | Lgt2 | ||||||
Keywords | TRANSFERASE / Glucosyltransferase / bacterial effector | ||||||
Function / homology | Glycosyltransferase family 88 / Glycosyltransferase family 88 / Glucosyltransferase Lgt2 Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å | ||||||
Authors | Chen, T.T. / Ouyang, S.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Small Struct / Year: 2023 Title: Structural Basis for the Action Mechanism of Legionella Glycosyltransferase. Authors: Chen, T.T. / Zheng, S.R. / Tian, L. / Lv, S.L. / Zhong, W.H. / Li, X.L. / Zhang, D.D. / Zheng, X.X. / Ouyang, S.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xgv.cif.gz | 259.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xgv.ent.gz | 205.2 KB | Display | PDB format |
PDBx/mmJSON format | 7xgv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xgv_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
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Full document | 7xgv_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 7xgv_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 7xgv_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/7xgv ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgv | HTTPS FTP |
-Related structure data
Related structure data | 7xgxC 8hcyC 3jszS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 73771.242 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: C3927_14430 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F0H5 #2: 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: 2.45 Å3/Da / Density % sol: 49.82 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG3350, Calcium acetate hydrate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.979 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Oct 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→29.22 Å / Num. obs: 66028 / % possible obs: 97.3 % / Redundancy: 2 % / Biso Wilson estimate: 44.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02234 / Rpim(I) all: 0.02234 / Rrim(I) all: 0.0316 / Net I/σ(I): 16.27 |
Reflection shell | Resolution: 2.27→2.351 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2474 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 64406 / CC1/2: 0.951 / Rpim(I) all: 0.2474 / Rrim(I) all: 0.3499 / % possible all: 92.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3JSZ Resolution: 2.27→29.22 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30.67 / 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: 117.73 Å2 / Biso mean: 62.071 Å2 / Biso min: 28.55 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.27→29.22 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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