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- PDB-7wx6: A Legionella acetyltransferase VipF -

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Basic information

Entry
Database: PDB / ID: 7wx6
TitleA Legionella acetyltransferase VipF
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / Toxin / acetyltransferase
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / CHLORAMPHENICOL / COENZYME A / N-acetyltransferase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.273 Å
AuthorsChen, T.T. / Lin, Y.L. / Chen, Z. / Han, A.D.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770803 China
National Natural Science Foundation of China (NSFC)81861138047 China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural basis for the acetylation mechanism of the Legionella effector VipF.
Authors: Chen, T.T. / Lin, Y. / Zhang, S. / Han, A.
History
DepositionFeb 14, 2022Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 14, 2022ID: 7C4G
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0154
Polymers35,1571
Non-polymers1,8583
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-6 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.047, 84.525, 105.547
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Protein N-acetyltransferase / VipF


Mass: 35157.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: vipF, C3927_15730, DI026_06115 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5C8M4
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG8000,EG,HEPES PH7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Jul 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.273→52.773 Å / Num. obs: 14810 / % possible obs: 97.43 % / Redundancy: 13.1 % / CC1/2: 0.983 / Net I/σ(I): 33.846
Reflection shellResolution: 2.273→2.32 Å / Num. unique obs: 14810 / CC1/2: 0.945

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WX5

7wx5


Resolution: 2.273→52.773 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0.34 / Phase error: 24.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2526 1482 10.01 %
Rwork0.2211 13328 -
obs0.2242 14810 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.77 Å2 / Biso mean: 33.5335 Å2 / Biso min: 8.7 Å2
Refinement stepCycle: final / Resolution: 2.273→52.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2160 0 116 105 2381
Biso mean--49.44 31.62 -
Num. residues----267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092324
X-RAY DIFFRACTIONf_angle_d1.1373152
X-RAY DIFFRACTIONf_chiral_restr0.057346
X-RAY DIFFRACTIONf_plane_restr0.006386
X-RAY DIFFRACTIONf_dihedral_angle_d16.281356
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.273-2.34630.33521250.303112792
2.3463-2.43020.31541260.2782114194
2.4302-2.52750.32341300.2465116595
2.5275-2.64250.28081340.2379120197
2.6425-2.78180.32221320.2194119598
2.7818-2.95610.251350.2152120899
2.9561-3.18430.30451350.23121999
3.1843-3.50470.23081390.2122124599
3.5047-4.01170.23441390.20881251100
4.0117-5.05370.18481390.18121255100
5.0537-52.7730.24461480.22931321100
Refinement TLS params.Method: refined / Origin x: -13.3867 Å / Origin y: -15.4362 Å / Origin z: 11.7052 Å
111213212223313233
T0.1112 Å2-0.0141 Å2-0.0013 Å2-0.1302 Å2-0.0094 Å2--0.0994 Å2
L0.9276 °2-0.8915 °2-1.0873 °2-1.2043 °20.8714 °2--0.8422 °2
S0.0178 Å °-0.0643 Å °0.0162 Å °-0.0637 Å °0.0333 Å °0.0103 Å °-0.0985 Å °0.0956 Å °-0.0161 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 280
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 116

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