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- PDB-7wx7: complex of a legionella acetyltransferase VipF and COA/ACO -

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Basic information

Entry
Database: PDB / ID: 7wx7
Titlecomplex of a legionella acetyltransferase VipF and COA/ACO
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / Toxin / acetyltransferase
Function / homology: / Acetyltransferase (GNAT) family / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / ACETYL COENZYME *A / COENZYME A / GNAT family N-acetyltransferase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.781 Å
AuthorsChen, T.T. / Lin, Y.L. / Zhang, S.J. / 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
SupersessionFeb 22, 2023ID: 7C4F
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: 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)36,7343
Polymers35,1571
Non-polymers1,5772
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-4 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.762, 82.426, 104.839
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-501-

HOH

21A-508-

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.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: PEG3350,BIS-TRIS5.5

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Data collection

DiffractionMean temperature: 233 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.781→54.124 Å / Num. obs: 29485 / % possible obs: 99.89 % / Redundancy: 11.9 % / CC1/2: 0.927 / Net I/σ(I): 8.7
Reflection shellResolution: 1.781→1.81 Å / Num. unique obs: 29485 / CC1/2: 0.927

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WX6

7wx6


Resolution: 1.781→54.124 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 23.96 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2237 2000 6.78 %
Rwork0.2076 27485 -
obs0.2086 29485 97.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.53 Å2 / Biso mean: 40.2328 Å2 / Biso min: 16.66 Å2
Refinement stepCycle: final / Resolution: 1.781→54.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 99 112 2511
Biso mean--42.76 43.06 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012462
X-RAY DIFFRACTIONf_angle_d1.1773346
X-RAY DIFFRACTIONf_chiral_restr0.064363
X-RAY DIFFRACTIONf_plane_restr0.006417
X-RAY DIFFRACTIONf_dihedral_angle_d14.1061446
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.781-1.82520.33441300.3033179791
1.8252-1.87460.3021360.2674186994
1.8746-1.92970.29721350.2561185695
1.9297-1.9920.29131420.2348194598
1.992-2.06320.23851400.2312192598
2.0632-2.14580.25361440.2357196598
2.1458-2.24350.27141420.2288196399
2.2435-2.36180.26791450.22031998100
2.3618-2.50970.24331440.2288197999
2.5097-2.70350.23991450.2171991100
2.7035-2.97560.22161460.22772005100
2.9756-3.40610.211490.20952036100
3.4061-4.2910.20521470.18322031100
4.291-54.1240.18961550.1812212599
Refinement TLS params.Method: refined / Origin x: 84.8626 Å / Origin y: 179.3499 Å / Origin z: 11.6531 Å
111213212223313233
T0.1895 Å2-0.0408 Å2-0.0045 Å2-0.1959 Å2-0.0351 Å2--0.1937 Å2
L0.5916 °2-0.4291 °20.4335 °2-1.3066 °2-1.4491 °2--2.3908 °2
S-0.0278 Å °-0.0455 Å °0.0258 Å °-0.0805 Å °-0.039 Å °-0.086 Å °0.2088 Å °-0.1345 Å °-0.0038 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-4 - 283
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 121

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