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- PDB-8yuf: Crystal structure of HEPN (Q64A) toxin -

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Basic information

Entry
Database: PDB / ID: 8yuf
TitleCrystal structure of HEPN (Q64A) toxin
ComponentsNucleotidyltransferase
KeywordsTOXIN / HEPN-MNT module
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsJin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A5A2024425 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1F1A1050961 Korea, Republic Of
CitationJournal: To Be Published
Title: Structural and functional study of HEPN-MNT module from Legionella pneumophila
Authors: Jin, C. / Jeon, C. / Kim, D.H. / Lee, B.J.
History
DepositionMar 27, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotidyltransferase
B: Nucleotidyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5093
Polymers32,4852
Non-polymers241
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-17 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.774, 43.772, 163.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Nucleotidyltransferase


Mass: 16242.289 Da / Num. of mol.: 2 / Mutation: Q64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_14745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA45B366
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Lithium acetate dehydrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.02 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.59→43.77 Å / Num. obs: 67303 / % possible obs: 83 % / Redundancy: 4.06 % / Biso Wilson estimate: 21.12 Å2 / CC1/2: 0.997 / Net I/σ(I): 11.8
Reflection shellResolution: 1.59→1.69 Å / Num. unique obs: 8590 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→42.28 Å / SU ML: 0.1816 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.1894
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 3720 5.53 %
Rwork0.1879 63510 -
obs0.1893 67230 83.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.45 Å2
Refinement stepCycle: LAST / Resolution: 1.59→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 1 306 2505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082244
X-RAY DIFFRACTIONf_angle_d0.84343021
X-RAY DIFFRACTIONf_chiral_restr0.0557319
X-RAY DIFFRACTIONf_plane_restr0.0076392
X-RAY DIFFRACTIONf_dihedral_angle_d12.4856823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.610.29091110.25651729X-RAY DIFFRACTION60.43
1.61-1.640.25781060.22171874X-RAY DIFFRACTION65.69
1.64-1.660.27631100.22341947X-RAY DIFFRACTION68.84
1.66-1.680.2921070.18511874X-RAY DIFFRACTION65.68
1.68-1.710.21861170.20671907X-RAY DIFFRACTION68.49
1.71-1.730.25311180.19161927X-RAY DIFFRACTION68.69
1.73-1.760.20841160.18591949X-RAY DIFFRACTION67.82
1.76-1.790.18941270.18451951X-RAY DIFFRACTION71.24
1.79-1.820.24171180.19762020X-RAY DIFFRACTION69.6
1.82-1.860.2241150.20362118X-RAY DIFFRACTION75.57
1.86-1.90.25061150.2122206X-RAY DIFFRACTION76
1.9-1.940.25771410.20472150X-RAY DIFFRACTION78.24
1.94-1.980.29151350.22351X-RAY DIFFRACTION81.8
1.98-2.030.2871350.19332351X-RAY DIFFRACTION84.19
2.03-2.090.18761380.19432462X-RAY DIFFRACTION85.84
2.09-2.150.18791410.1832488X-RAY DIFFRACTION88.97
2.15-2.220.22561580.17612580X-RAY DIFFRACTION89.92
2.22-2.30.21871570.18572604X-RAY DIFFRACTION91.51
2.3-2.390.1681540.19452669X-RAY DIFFRACTION95.63
2.39-2.50.25651510.18472753X-RAY DIFFRACTION97.25
2.5-2.630.2681640.19532771X-RAY DIFFRACTION97.77
2.63-2.80.21391700.20062806X-RAY DIFFRACTION98.61
2.8-3.010.24711450.19532779X-RAY DIFFRACTION98.55
3.01-3.310.21941750.18572755X-RAY DIFFRACTION97.67
3.32-3.790.19781570.18092824X-RAY DIFFRACTION99.3
3.79-4.780.16061630.16762858X-RAY DIFFRACTION99.97
4.78-42.280.19471760.18562807X-RAY DIFFRACTION99.77
Refinement TLS params.Method: refined / Origin x: 2.89348812029 Å / Origin y: -8.13212243558 Å / Origin z: -20.4590308902 Å
111213212223313233
T0.104470940278 Å20.00174547729774 Å2-0.029642077444 Å2-0.124435601005 Å20.0237938152834 Å2--0.140675017529 Å2
L0.881586698674 °2-0.164406970287 °20.196888055164 °2-0.945458739993 °2-0.200143885187 °2--1.01453625254 °2
S0.0176104460745 Å °-0.0232319955539 Å °-0.0170265179569 Å °-0.0158659073262 Å °0.0171172265737 Å °0.0497797446202 Å °0.0418116864259 Å °-0.0569820126974 Å °-0.0315693551781 Å °
Refinement TLS groupSelection details: all

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