+Open data
-Basic information
Entry | Database: PDB / ID: 6k3b | ||||||
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Title | Crystal structure of Lpg2147-Lpg2149 complex | ||||||
Components |
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Keywords | ANTITOXIN / metaeffector / complex / deamidase | ||||||
Function / homology | : / MvcA insertion domain / Lpg2149 family Dot/Icm T4SS effector / Uncharacterized protein / Uncharacterized protein / MvcA insertion domain-containing protein Function and homology information | ||||||
Biological species | Legionella pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.974 Å | ||||||
Authors | Mu, Y. / Wang, Y. / Han, Y. / Li, D. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural insights into the mechanism and inhibition of transglutaminase-induced ubiquitination by the Legionella effector MavC. Authors: Mu, Y. / Wang, Y. / Huang, Y. / Li, D. / Han, Y. / Chang, M. / Fu, J. / Xie, Y. / Ren, J. / Wang, H. / Zhang, Y. / Luo, Z.Q. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k3b.cif.gz | 122.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k3b.ent.gz | 91.3 KB | Display | PDB format |
PDBx/mmJSON format | 6k3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k3b_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 6k3b_full_validation.pdf.gz | 437.4 KB | Display | |
Data in XML | 6k3b_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6k3b_validation.cif.gz | 35 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k3/6k3b ftp://data.pdbj.org/pub/pdb/validation_reports/k3/6k3b | HTTPS FTP |
-Related structure data
Related structure data | 6kfpC 6kg6C 5dpoS 5tscS 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: 43534.148 Da / Num. of mol.: 1 / Mutation: C74A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_10720 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6F4I5, UniProt: Q5ZTL4*PLUS |
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#2: Protein | Mass: 12790.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3928_10970 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S6EWM8, UniProt: Q5ZTL2*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG3350, ammonium nitrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.974→50 Å / Num. obs: 39377 / % possible obs: 99.57 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 1.974→2.05 Å / Rmerge(I) obs: 0.363 / Num. unique obs: 3744 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TSC, 5DPO Resolution: 1.974→37.111 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 20.56
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.974→37.111 Å
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Refine LS restraints |
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LS refinement shell |
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