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- PDB-5nh2: Bartonella henselae BepA Fic domain in complex with its antitoxin... -

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Basic information

Entry
Database: PDB / ID: 5nh2
TitleBartonella henselae BepA Fic domain in complex with its antitoxin homologue BiaA
Components
  • Adenosine monophosphate-protein transferase
  • Uncharacterized protein
KeywordsTRANSFERASE / Fic domain
Function / homology
Function and homology information


negative regulation of protein adenylylation / AMPylase activity / protein adenylylation / protein adenylyltransferase / symbiont-mediated suppression of host apoptosis / regulation of cell division / extracellular region / 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 proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Antitoxin VbhA domain-containing protein / Protein adenylyltransferase
Similarity search - Component
Biological speciesBartonella henselae str. Houston-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.321 Å
AuthorsDietz, N. / Schirmer, T.
CitationJournal: To Be Published
Title: Bartonella henselae BepA Fic domain in complex with its antitoxin homologue BiaA
Authors: Dietz, N. / Schirmer, T.
History
DepositionMar 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: Adenosine monophosphate-protein transferase
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1113
Polymers42,0872
Non-polymers241
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-19 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.034, 56.152, 136.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Adenosine monophosphate-protein transferase / AMPylator


Mass: 34425.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae str. Houston-1 (bacteria)
Gene: bepA, BH13370 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI
References: UniProt: Q6G2A9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein Uncharacterized protein


Mass: 7661.802 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae str. Houston-1 (bacteria)
Gene: BH13360 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: A0A0H3LZG7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.6 / Details: 0.2 M di-Sodium malonate, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 13, 2016 / Details: q
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.321→43.375 Å / Num. obs: 15699 / % possible obs: 94 % / Redundancy: 7.7 % / Biso Wilson estimate: 37.4 Å2 / CC1/2: 0.998 / Net I/σ(I): 18.08

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vza

2vza


Resolution: 2.321→43.375 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2622 1570 10 %
Rwork0.1787 --
obs0.1872 15699 94.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.321→43.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 1 105 2862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132813
X-RAY DIFFRACTIONf_angle_d1.2343796
X-RAY DIFFRACTIONf_dihedral_angle_d17.0861701
X-RAY DIFFRACTIONf_chiral_restr0.066415
X-RAY DIFFRACTIONf_plane_restr0.009497
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3206-2.39550.32691230.22261108X-RAY DIFFRACTION83
2.3955-2.48110.30051310.21311170X-RAY DIFFRACTION89
2.4811-2.58050.34311330.2191208X-RAY DIFFRACTION90
2.5805-2.69790.34071370.20551223X-RAY DIFFRACTION92
2.6979-2.84010.35991410.20551271X-RAY DIFFRACTION93
2.8401-3.0180.2651410.19791281X-RAY DIFFRACTION97
3.018-3.25090.29141470.19881313X-RAY DIFFRACTION97
3.2509-3.5780.25271480.181332X-RAY DIFFRACTION98
3.578-4.09540.2481520.16211375X-RAY DIFFRACTION99
4.0954-5.15840.2181540.13911381X-RAY DIFFRACTION100
5.1584-43.38250.23161630.17981467X-RAY DIFFRACTION100
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)
13.4617-0.948-1.52482.13270.43094.6140.10420.25970.3408-0.15250.07880.0166-0.535-0.7472-0.06230.2450.0211-0.00170.2588-0.01880.39766.225919.805932.1878
22.4334-0.8342-0.26861.61621.28574.9319-0.00770.0943-0.37840.1476-0.03230.24740.3871-0.2668-0.01550.3002-0.08290.06610.262-0.02410.349312.58278.611237.4613
33.0545-1.7385-1.57182.7404-0.91582.638-0.1844-0.05590.4985-0.08730.0175-0.4208-0.6860.2215-0.20470.472-0.03720.08570.2722-0.02460.508524.859320.629230.29
41.8973-0.104-0.15632.98011.87065.4817-0.0135-0.0597-0.23870.34820.2573-0.16870.4710.4539-0.04590.29380.06550.00620.32440.020.41827.650110.124848.7324
51.19770.6242-0.36262.88210.88052.98910.0243-0.1839-0.02030.2386-0.11130.0359-0.0968-0.01960.05260.24290.01350.04410.33560.01170.257819.726323.898852.8362
62.09991.2-0.13333.61021.84354.5529-0.1909-0.13450.19690.66890.04760.0806-1.30510.3567-0.0080.5613-0.02480.07240.37240.00060.402220.661437.702760.1388
73.59910.2328-1.37753.91020.62527.00650.54-0.58040.41630.8016-0.0380.5285-1.27840.0013-0.08180.6245-0.03370.03070.4044-0.08950.386321.532838.334864.0013
82.45320.4727-0.52171.23971.52873.72150.181-0.85750.24861.50660.00530.1328-1.03650.0239-0.10311.1951-0.0515-0.0620.5812-0.12350.517823.531443.573371.9445
95.40362.4573-3.86293.2913-1.85992.74620.3459-0.71360.11440.5697-0.4159-0.18080.35210.40110.12660.4173-0.1296-0.02160.3756-0.06990.31275.470321.55554.9682
105.60461.076-0.59975.6181-0.37763.17160.1733-0.61710.57650.7687-0.48791.059-0.0372-0.26920.14520.2953-0.03210.14910.3435-0.10780.3891-2.591125.151849.2233
118.2437-0.15551.23098.7288-1.31016.12020.07170.7226-0.1681-0.0402-0.14490.53870.5329-0.7330.18890.27360.02680.04810.5028-0.13360.4402-7.479418.13444.2345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 115 )
4X-RAY DIFFRACTION4chain 'A' and (resid 116 through 158 )
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 236 )
6X-RAY DIFFRACTION6chain 'A' and (resid 237 through 264 )
7X-RAY DIFFRACTION7chain 'A' and (resid 265 through 281 )
8X-RAY DIFFRACTION8chain 'A' and (resid 282 through 302 )
9X-RAY DIFFRACTION9chain 'B' and (resid 14 through 35 )
10X-RAY DIFFRACTION10chain 'B' and (resid 36 through 56 )
11X-RAY DIFFRACTION11chain 'B' and (resid 57 through 69 )

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