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- PDB-3zc7: VbhT Fic protein from Bartonella schoenbuchensis in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3zc7
TitleVbhT Fic protein from Bartonella schoenbuchensis in complex with VbhA antitoxin and ATP
Components
  • ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE VBHT
  • ANTITOXIN VBHA
KeywordsTRANSFERASE/ANTITOXIN / TRANSFERASE-ANTITOXIN COMPLEX / AMPYLATION / ADENYLYLATION
Function / homology
Function and homology information


negative regulation of protein adenylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / magnesium ion binding / protein homodimerization activity / ATP binding
Similarity search - Function
Antitoxin VbhA-like / Antitoxin VbhA / Antitoxin VbhA / Antitoxin VbhA-like / Antitoxin VbhA domain superfamily / Bartonella effector protein, BID domain / BID domain of Bartonella effector protein (Bep) / Fido-like domain / Fic-like fold / Fido-like domain superfamily ...Antitoxin VbhA-like / Antitoxin VbhA / Antitoxin VbhA / Antitoxin VbhA-like / Antitoxin VbhA domain superfamily / Bartonella effector protein, BID domain / BID domain of Bartonella effector protein (Bep) / Fido-like domain / Fic-like fold / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Protein adenylyltransferase VbhT / Antitoxin VbhA
Similarity search - Component
Biological speciesBARTONELLA SCHOENBUCHENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGoepfert, A. / Schirmer, T.
CitationJournal: Plos One / Year: 2013
Title: Conserved Inhibitory Mechanism and Competent ATP Binding Mode for Adenylyltransferases with Fic Fold.
Authors: Goepfert, A. / Stanger, F.V. / Dehio, C. / Schirmer, T.
History
DepositionNov 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE VBHT
B: ANTITOXIN VBHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6323
Polymers37,1252
Non-polymers5071
Water4,071226
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-18.2 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.460, 40.620, 73.740
Angle α, β, γ (deg.)90.00, 121.55, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2084-

HOH

21A-2085-

HOH

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Components

#1: Protein ADENOSINE MONOPHOSPHATE-PROTEIN TRANSFERASE VBHT / AMPYLATOR VBHT / VBHT TOXIN


Mass: 29745.154 Da / Num. of mol.: 1 / Fragment: FIC DOMAIN, RESIDUES 1-248 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BARTONELLA SCHOENBUCHENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: E6Z0R3, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Protein ANTITOXIN VBHA


Mass: 7379.365 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-62
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BARTONELLA SCHOENBUCHENSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E6Z0R4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.94 Å3/Da / Density % sol: 36.5 % / Description: NONE
Crystal growpH: 6.5
Details: 15% PEG 4000, 0.1M MES PH 6.5. THEN SOAKED WITH 5MM ATP AND 5MM MGCL2U.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→45.36 Å / Num. obs: 15824 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.87
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 4.89 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 5.86 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SHG

3shg


Resolution: 2.1→15 Å / SU ML: 0.2 / σ(F): 2.01 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 815 5.2 %
Rwork0.1646 --
obs0.1679 15769 99.15 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 3.3513 Å2 / ksol: 1.0016 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 31 226 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072244
X-RAY DIFFRACTIONf_angle_d1.0083028
X-RAY DIFFRACTIONf_dihedral_angle_d17.904897
X-RAY DIFFRACTIONf_chiral_restr0.071318
X-RAY DIFFRACTIONf_plane_restr0.004395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1001-2.23120.24761470.18552342X-RAY DIFFRACTION95
2.2312-2.40290.25481430.17472503X-RAY DIFFRACTION100
2.4029-2.64350.24121250.16792478X-RAY DIFFRACTION100
2.6435-3.02330.26691250.17592525X-RAY DIFFRACTION100
3.0233-3.79880.20571390.15192529X-RAY DIFFRACTION100
3.7988-15.00020.21471360.1582577X-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)
13.2286-1.3681.36273.0981-0.75052.0991-0.1141-0.1171-0.55470.24230.16950.12650.68330.1829-0.01880.31810.17940.1480.1017-0.01590.2746-0.9951-41.6066.4758
23.35991.72770.9075.23160.6764.8951-0.1267-0.1273-0.18340.1861-0.0473-0.26680.29120.19840.10410.08580.05350.00120.17710.02450.0692-3.3772-28.854318.7403
34.6226-2.25560.49832.3351-0.52551.5916-0.03470.09030.2875-0.06960.0728-0.1601-0.11920.1627-0.05890.0591-0.01770.0230.0878-0.0330.0671-7.2199-22.39876.8713
44.9842-2.00022.01594.00371.77793.4664-0.0045-0.4848-0.9780.5178-0.10090.37360.5637-0.52320.07820.1957-0.1550.04250.2046-0.02830.2929-18.641-36.91932.381
51.965-1.9282-0.5372.82710.54970.8398-0.00180.26830.02510.066-0.0498-0.0061-0.0709-0.39510.03070.16140.0019-0.03030.19250.09360.128-22.274-17.66421.8157
61.2047-0.1078-0.19191.0235-0.27241.6805-0.0783-0.0081-0.01370.09990.11830.0377-0.1325-0.3256-0.02630.06140.00960.00050.10370.03010.0857-20.1045-21.752913.9977
72.29951.0931-0.33923.1144-1.13088.6442-0.02190.017-0.15590.2232-0.1937-0.38830.0947-0.66920.19520.1806-0.0532-0.00170.1507-0.08450.2171-26.0114-33.345615.7466
82.82961.36030.73474.12494.36046.6846-0.02930.1988-0.07740.1682-0.09420.09460.226-0.60960.11660.11470.03620.00670.23330.0250.1244-29.5806-25.145817.1991
90.64351.3788-0.96095.2541-4.81245.41-0.16380.23380.61240.1054-0.0454-0.3377-1.19880.73830.1570.576-0.05440.05730.43840.14450.4288-17.8402-5.314915.4312
102.66233.26232.54025.83173.83543.9446-0.07540.03790.2749-0.2313-0.13930.298-0.24040.21530.20970.09420.00680.00790.08710.02940.0965-9.143-19.165528.1636
114.1112.77131.93774.36652.81652.93810.0993-0.3038-0.2470.1848-0.0128-0.32640.30220.4067-0.05820.14670.084-0.0220.27660.01240.1341-1.0126-26.300328.3579
123.528-3.27250.41064.5823-0.87892.65590.04850.0531-0.0333-0.001-0.0344-0.20880.51610.7744-0.05020.13710.1635-0.03310.5617-0.01360.19898.3877-30.30421.3544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 8 THROUGH 27 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 28 THROUGH 48 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 49 THROUGH 78 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 79 THROUGH 92 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 93 THROUGH 117 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 118 THROUGH 167 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 168 THROUGH 179 )
8X-RAY DIFFRACTION8CHAIN A AND (RESID 180 THROUGH 193 )
9X-RAY DIFFRACTION9CHAIN A AND (RESID 194 THROUGH 206 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 0 THROUGH 24 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 25 THROUGH 45 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 46 THROUGH 62 )

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