+Open data
-Basic information
Entry | Database: PDB / ID: 7xql | ||||||
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Title | complex structure of LegA15 with GNP | ||||||
Components | Ankyrin repeat-containing protein | ||||||
Keywords | TOXIN / Legionella penumophila effector / GTPase | ||||||
Function / homology | Domain of unknown function DUF3447 / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ankyrin repeat-containing protein Function and homology information | ||||||
Biological species | Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.272 Å | ||||||
Authors | Chen, T.T. / Lin, Y.L. | ||||||
Funding support | China, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Atypical Legionella GTPase effector hijacks host vesicular transport factor p115 to regulate host lipid droplet. Authors: Chen, T.T. / Lin, Y. / Zhang, S. / Liu, S. / Song, L. / Zhong, W. / Luo, Z.Q. / Han, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xql.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xql.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 7xql.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xql_validation.pdf.gz | 934.6 KB | Display | wwPDB validaton report |
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Full document | 7xql_full_validation.pdf.gz | 944 KB | Display | |
Data in XML | 7xql_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 7xql_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/7xql ftp://data.pdbj.org/pub/pdb/validation_reports/xq/7xql | HTTPS FTP |
-Related structure data
Related structure data | 7ew8SC 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: 51952.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria) Gene: legA15, lpg2456 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZSR1 #2: Chemical | ChemComp-GNP / | #3: Water | ChemComp-HOH / | 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: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: Ammonium acetate, sodium citrate pH 5.6, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 14, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 2.272→34.602 Å / Num. obs: 46821 / % possible obs: 99.1 % / Redundancy: 2 % / Biso Wilson estimate: 36.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.02335 / Rpim(I) all: 0.02335 / Rrim(I) all: 0.03302 / Net I/σ(I): 18.55 |
Reflection shell | Resolution: 2.272→2.353 Å / Redundancy: 2 % / Rmerge(I) obs: 0.09617 / Mean I/σ(I) obs: 6.86 / Num. unique obs: 4427 / CC1/2: 0.973 / Rpim(I) all: 0.09617 / Rrim(I) all: 0.136 / % possible all: 95.08 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EW8 Resolution: 2.272→34.602 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / Phase error: 23.35 / 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: 96.47 Å2 / Biso mean: 42.6778 Å2 / Biso min: 21.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.272→34.602 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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