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- PDB-5eu0: FIC domain of Bep1 from Bartonella rochalimae in complex with BiaA -

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Basic information

Entry
Database: PDB / ID: 5eu0
TitleFIC domain of Bep1 from Bartonella rochalimae in complex with BiaA
Components
  • Bartonella effector protein (Bep) substrate of VirB T4SS
  • antitoxin 1
KeywordsTOXIN / AMPylation / adenylylation / Fic proteins / toxin-antitoxin complex
Function / homology
Function and homology information


negative regulation of protein adenylylation / protein adenylyltransferase / regulation of cell division / nucleotidyltransferase activity / ATP binding
Similarity search - Function
Antitoxin VbhA-like / Antitoxin VbhA domain superfamily / BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. ...Antitoxin VbhA-like / Antitoxin VbhA domain superfamily / BepA, intracellular delivery domain / Intracellular delivery domain / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
protein adenylyltransferase / Antitoxin VbhA domain-containing protein
Similarity search - Component
Biological speciesBartonella rochalimae ATCC BAA-1498 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsGoepfert, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation3100-138414 Switzerland
CitationJournal: to be published
Title: Molecular basis for Rho-family GTPase discrimination by a bacterial virulence factor
Authors: Dietz, N. / Harms, A. / Sorg, I. / Mas, G. / Goepfert, A. / Hiller, S. / Schirmer, T. / Dehio, C.
History
DepositionNov 18, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2017Group: Structure summary
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bartonella effector protein (Bep) substrate of VirB T4SS
B: antitoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6374
Polymers33,4452
Non-polymers1922
Water4,828268
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-42 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.130, 73.130, 130.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 25997.557 Da / Num. of mol.: 1 / Fragment: FIC domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella rochalimae ATCC BAA-1498 (bacteria)
Gene: BARRO_10061 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YJU0
#2: Protein antitoxin 1 / Bia1


Mass: 7447.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella rochalimae ATCC BAA-1498 (bacteria)
Gene: BARRO_50056, O99_01280 / Plasmid: pRSFDuet1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E6YLF5
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M HEPES pH7.5, 2.3M AMMONIUM SULFATE, 2% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→73.1 Å / Num. obs: 47293 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 21 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rrim(I) all: 0.146 / Χ2: 1.013 / Net I/σ(I): 16.29 / Num. measured all: 547927
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.027 / Mean I/σ(I) obs: 1.31 / Num. measured obs: 6418 / Num. possible: 634 / Num. unique obs: 633 / CC1/2: 1 / Rrim(I) all: 0.028 / Rejects: 0 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER-TNT2.11.7refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SHG

3shg


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.083 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.077
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2364 5 %RANDOM
Rwork0.189 ---
obs0.19 47280 99.8 %-
Displacement parametersBiso max: 97.71 Å2 / Biso mean: 25.19 Å2 / Biso min: 8.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.4786 Å20 Å20 Å2
2--0.4786 Å20 Å2
3----0.9573 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 10 268 2444
Biso mean--40.54 34.37 -
Num. residues----268
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d783SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes66HARMONIC2
X-RAY DIFFRACTIONt_gen_planes313HARMONIC5
X-RAY DIFFRACTIONt_it2222HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion293SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2847SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2222HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3004HARMONIC20.88
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion15.52
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 169 4.99 %
Rwork0.291 3220 -
all-3389 -
obs--98.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.36270.11340.2241.3541-0.02831.0167-0.00380.0072-0.0238-0.00280.0026-0.18620.03660.10040.0012-0.04340.022-0.0148-0.0833-0.0037-0.008227.386259.289649.2447
21.4451-0.791-0.27372.31310.74741.416-0.06-0.05840.0393-0.02330.1-0.3454-0.04390.2092-0.04-0.0432-0.0031-0.0081-0.071-0.01430.042635.900678.040156.767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A19 - 231
2X-RAY DIFFRACTION2{ B|* }B13 - 67

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