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- PDB-7wx5: a Legionella acetyltransferase effector VipF -

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Basic information

Entry
Database: PDB / ID: 7wx5
Titlea Legionella acetyltransferase effector 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 / ACETYL COENZYME *A / N-acetyltransferase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.392 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: 7C4E
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 1.2Apr 3, 2024Group: 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)36,7763
Polymers35,1571
Non-polymers1,6192
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-8 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.977, 85.594, 105.195
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate,Bis-tris ph5.5,PEG10000

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97853 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.392→55.088 Å / Num. obs: 13149 / % possible obs: 100 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.108 / Χ2: 1.008 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.392-2.4413.80.1726450.9880.0480.1791.139100
2.44-2.4913.90.1626430.9880.0450.1681.136100
2.49-2.5313.80.1596460.990.0450.1661.129100
2.53-2.5913.60.1566420.990.0430.1621.117100
2.59-2.6413.40.156430.990.0420.1561.122100
2.64-2.713.20.1436620.9910.0410.1491.102100
2.7-2.7712.80.1416420.9920.0410.1471.106100
2.77-2.8512.50.1376570.990.040.1431.118100
2.85-2.9313.70.1356280.9930.0380.141.102100
2.93-3.0213.80.136540.990.0360.1351.07100
3.02-3.1313.80.1216660.9940.0340.1251.026100
3.13-3.2613.70.126430.9930.0330.1251.083100
3.26-3.4113.50.1146580.9940.0320.1191.036100
3.41-3.5812.90.1116490.9940.0310.1151.024100
3.58-3.8112.70.1096590.9930.0310.1131.027100
3.81-4.113.90.1026670.9950.0280.1060.934100
4.1-4.5213.60.0976640.9960.0270.1010.896100
4.52-5.17130.0896800.9940.0260.0930.769100
5.17-6.5112.70.0846760.9930.0250.0870.61100
6.51-50120.0837250.9920.0250.0870.61599.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 01ZP

Resolution: 2.392→55.088 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.7 / Phase error: 22.44 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2323 1315 10 %
Rwork0.2181 11831 -
obs0.2195 13146 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.64 Å2 / Biso mean: 37.5205 Å2 / Biso min: 10.54 Å2
Refinement stepCycle: final / Resolution: 2.392→55.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 102 89 2536
Biso mean--48.43 34.08 -
Num. residues----288
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052503
X-RAY DIFFRACTIONf_angle_d0.9253401
X-RAY DIFFRACTIONf_chiral_restr0.052368
X-RAY DIFFRACTIONf_plane_restr0.006425
X-RAY DIFFRACTIONf_dihedral_angle_d15.2481473
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3923-2.48810.26921410.25031274
2.4881-2.60140.25471450.22591303
2.6014-2.73850.24451430.23341283
2.7385-2.91010.3221460.23221314
2.9101-3.13470.25941460.24761312
3.1347-3.45010.24321430.22251291
3.4501-3.94930.22961480.21631330
3.9493-4.97520.19361470.17961328
4.9752-55.0880.20191560.20191396
Refinement TLS params.Method: refined / Origin x: 84.5564 Å / Origin y: 100.0685 Å / Origin z: 11.6756 Å
111213212223313233
T0.1545 Å2-0.0368 Å2-0.0045 Å2-0.1313 Å2-0.0089 Å2--0.1368 Å2
L0.8111 °2-0.9004 °20.8112 °2-1.0637 °2-1.0768 °2--1.2107 °2
S0.0296 Å °-0.0592 Å °-0.0298 Å °-0.132 Å °0.0137 Å °0.0372 Å °0.2177 Å °-0.0766 Å °-0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-3 - 284
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allS1 - 89

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