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- PDB-7zbr: Crystal Structure of full-length Bartonella Effector protein 1 -

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Basic information

Entry
Database: PDB / ID: 7zbr
TitleCrystal Structure of full-length Bartonella Effector protein 1
ComponentsBartonella effector protein (Bep) substrate of VirB T4SS
KeywordsTOXIN / AMPylation / FIC / T4SS / VirD/B4 / domain insertion / Bartonella / Bartonella effector protein / Bep / BID / Bep intracellular delivery
Function / homologyBepA, 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
Function and homology information
Biological speciesBartonella clarridgeiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuber, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: To be published
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
DepositionMar 24, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bartonella effector protein (Bep) substrate of VirB T4SS


Theoretical massNumber of molelcules
Total (without water)63,8241
Polymers63,8241
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.492, 70.492, 213.961
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Bartonella effector protein (Bep) substrate of VirB T4SS


Mass: 63824.180 Da / Num. of mol.: 1 / Fragment: full-length
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella clarridgeiae (bacteria) / Strain: CIP 104772 / 73 / Gene: BARCL_0069 / Plasmid: pET26 derived / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YFW2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 3→3.06 Å / Num. unique obs: 1271 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
Aimlessdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NPS, 4YK3

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
RfactorNum. reflection% reflection
Rfree0.303 2366 9.99 %
Rwork0.2701 21316 -
obs0.2734 13003 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.43 Å2 / Biso mean: 103.3999 Å2 / Biso min: 96.38 Å2
Refinement stepCycle: final / Resolution: 3→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4196 0 0 0 4196
Num. residues----531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.060.39981350.40361198133394
3.06-3.130.41441340.38041235136999
3.13-3.20.39251580.39821297145599
3.2-3.280.43981370.4031194133199
3.28-3.370.35921360.370812841420100
3.37-3.470.41251400.363212481388100
3.47-3.580.39521430.321412641407100
3.58-3.710.39431400.324612651405100
3.71-3.860.3511350.31412401375100
3.86-4.030.30641360.31112551391100
4.03-4.240.34671350.290612831418100
4.24-4.510.26141360.267112621398100
4.51-4.860.31181440.25241221136599
4.86-5.350.26081440.284712921436100
5.35-6.120.23571380.276112461384100
6.12-7.70.34271460.257312701416100
7.71-46.380.23511290.183812621391100

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