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- PDB-3shg: VBHT Fic protein from BARTONELLA SCHOENBUCHENSIS in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3shg
TitleVBHT Fic protein from BARTONELLA SCHOENBUCHENSIS in complex with VBHA antitoxin
Components
  • VbhA
  • VbhT
KeywordsTRANSFERASE/PROTEIN BINDING / AMPylation / adenylylation / toxin-antitoxin complex / Fic fold / AMP transfer / TRANSFERASE-PROTEIN BINDING complex
Function / homology
Function and homology information


negative regulation of protein adenylylation / AMPylase activity / protein adenylyltransferase / protein adenylylation / regulation of cell division / 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
L(+)-TARTARIC ACID / Protein adenylyltransferase VbhT / Antitoxin VbhA
Similarity search - Component
Biological speciesBartonella schoenbuchensis R1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsGoepfert, A. / Schirmer, T.
CitationJournal: Nature / Year: 2012
Title: Adenylylation control by intra- or intermolecular active-site obstruction in Fic proteins.
Authors: Engel, P. / Goepfert, A. / Stanger, F.V. / Harms, A. / Schmidt, A. / Schirmer, T. / Dehio, C.
History
DepositionJun 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: VbhT
B: VbhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6034
Polymers31,3032
Non-polymers3002
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-14 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.338, 40.371, 73.791
Angle α, β, γ (deg.)90.000, 121.400, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein VbhT


Mass: 24168.080 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: multiple cloning site 2
Source: (gene. exp.) Bartonella schoenbuchensis R1 (bacteria)
Gene: B11C_100026 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E6Z0R3
#2: Protein VbhA


Mass: 7135.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: multiple cloning site 1
Source: (gene. exp.) Bartonella schoenbuchensis R1 (bacteria)
Gene: B11C_100027 / Plasmid: pRSFDuet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E6Z0R4
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.16 Å3/Da / Density % sol: 43.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 23% w/v PEG 3350, 0.2M di-ammonium tartrate, vapor diffusion, hanging drop, temperature 293K

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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
ReflectionNumber: 155522
ReflectionResolution: 1.5→45.21 Å / Num. obs: 41211 / % possible obs: 96.24 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.77 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 9.0538
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique all% possible all
1.5-1.582.040.243.119438462274.81
1.58-1.683.450.233.1520236586899.59
1.68-1.794.040.183.93222235499100
1.79-1.944.110.135.01212055160100
1.94-2.124.110.14.9196104774100
2.12-2.374.120.086.94176984291100
2.37-2.744.130.086.97157223806100
2.74-3.354.130.078.46134613257100
3.35-4.744.110.0414103432515100
4.74-45.213.940.0316.595586141999.15

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.16 2010/01/06data scaling
MOSFLMdata reduction
PHENIXphasing
REFMAC5.5.0109refinement
RefinementResolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.562 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2069 5 %RANDOM
Rwork0.18 ---
obs0.181 41147 95.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 61.13 Å2 / Biso mean: 22.232 Å2 / Biso min: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å2-1.23 Å2
2--1.79 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2133 0 20 227 2380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212201
X-RAY DIFFRACTIONr_bond_other_d0.0010.021536
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.962973
X-RAY DIFFRACTIONr_angle_other_deg0.933687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9425267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8623.525122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09315388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9381524
X-RAY DIFFRACTIONr_chiral_restr0.080.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022505
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_mcbond_it2.1711.51310
X-RAY DIFFRACTIONr_mcbond_other0.7951.5535
X-RAY DIFFRACTIONr_mcangle_it3.24122103
X-RAY DIFFRACTIONr_scbond_it4.4823891
X-RAY DIFFRACTIONr_scangle_it6.9364.5869
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 92 -
Rwork0.336 1733 -
all-1825 -
obs--58.34 %

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