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- PDB-8xdj: Crystal structure of AMPylated HEPN toxin -

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Basic information

Entry
Database: PDB / ID: 8xdj
TitleCrystal structure of AMPylated HEPN toxin
ComponentsHEPN toxin
KeywordsTOXIN / ribonuclease
Function / homologyADENOSINE MONOPHOSPHATE
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionDec 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEPN toxin
B: HEPN toxin
C: HEPN toxin
D: HEPN toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,63510
Polymers65,1974
Non-polymers1,4376
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7820 Å2
ΔGint-32 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.199, 53.296, 88.021
Angle α, β, γ (deg.)90.000, 122.310, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
HEPN toxin


Mass: 16299.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 5.5 and 0.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 67341 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.04 Å2 / CC1/2: 0.996 / Net I/σ(I): 35.39
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 3325 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4418refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.01 Å / SU ML: 0.1987 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.224
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2043 1997 2.97 %
Rwork0.1759 65204 -
obs0.1768 67201 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 90 380 4811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01044526
X-RAY DIFFRACTIONf_angle_d1.10996101
X-RAY DIFFRACTIONf_chiral_restr0.0657645
X-RAY DIFFRACTIONf_plane_restr0.0086777
X-RAY DIFFRACTIONf_dihedral_angle_d9.7154598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.36421220.27513986X-RAY DIFFRACTION84.89
1.69-1.740.27991420.25494687X-RAY DIFFRACTION99.51
1.74-1.790.28741440.22824672X-RAY DIFFRACTION99.77
1.79-1.840.24821450.21194724X-RAY DIFFRACTION99.75
1.84-1.910.22941430.19554690X-RAY DIFFRACTION99.88
1.91-1.990.24361440.18514684X-RAY DIFFRACTION99.92
1.99-2.080.21991450.18014727X-RAY DIFFRACTION99.88
2.08-2.190.22111450.174720X-RAY DIFFRACTION99.92
2.19-2.320.18511450.16784705X-RAY DIFFRACTION99.81
2.32-2.50.20921440.17134714X-RAY DIFFRACTION99.63
2.5-2.760.22571440.18524727X-RAY DIFFRACTION99.55
2.76-3.150.23391450.17944729X-RAY DIFFRACTION99.67
3.15-3.970.16691450.15454753X-RAY DIFFRACTION99.65
3.97-29.010.17271440.16754686X-RAY DIFFRACTION95.99
Refinement TLS params.Method: refined / Origin x: 15.6076949432 Å / Origin y: 14.5894898825 Å / Origin z: 19.9247963448 Å
111213212223313233
T0.202013738668 Å20.00592858967774 Å20.0363887426669 Å2-0.173554111609 Å2-0.0177385229601 Å2--0.16287849139 Å2
L1.43297026084 °20.267346622724 °2-0.106874907748 °2-0.289118777806 °2-0.0642094362009 °2--0.273626377677 °2
S-0.0184220593433 Å °-0.0477863018108 Å °-0.0846060043451 Å °-0.0186938657263 Å °0.018100557253 Å °-0.0393648839269 Å °0.018755025121 Å °0.0126828413301 Å °-0.000819459906977 Å °
Refinement TLS groupSelection details: all

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