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Open data
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Basic information
Entry | Database: PDB / ID: 7zbr | ||||||
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Title | Crystal Structure of full-length Bartonella Effector protein 1 | ||||||
![]() | Bartonella effector protein (Bep) substrate of VirB T4SS | ||||||
![]() | TOXIN / AMPylation / FIC / T4SS / VirD/B4 / domain insertion / Bartonella / Bartonella effector protein / Bep / BID / Bep intracellular delivery | ||||||
Function / homology | BepA, intracellular delivery domain / Intracellular delivery domain / protein adenylyltransferase / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding, OB-fold / protein adenylyltransferase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Huber, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Full-length structure of a FIC effector protein from Bartonella reveals a novel structural domain Authors: Huber, M. / Wagner, A. / Reiners, J. / Seyfert, C.E.M. / Smits, S.H.J. / Schirmer, T. / Dehio, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.2 KB | Display | ![]() |
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PDB format | ![]() | 151.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.7 KB | Display | ![]() |
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Full document | ![]() | 423.9 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 24.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4npsS ![]() 4yk3S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 63824.180 Da / Num. of mol.: 1 / Fragment: full-length Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.84 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 100 mM Hepes pH 7.8, 0.175 mM LiCl and 20% v/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→46.38 Å / Num. obs: 13003 / % possible obs: 99.63 % / Redundancy: 12.8 % / Biso Wilson estimate: 110.18 Å2 / CC1/2: 0.993 / CC star: 0.998 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3→3.06 Å / Num. unique obs: 1271 / CC1/2: 0.335 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NPS, 4YK3 Resolution: 3→46.38 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.67 / 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: 114.43 Å2 / Biso mean: 103.3999 Å2 / Biso min: 96.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3→46.38 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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