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- PDB-8xeo: Crystal structure of MNT antitoxin -

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Basic information

Entry
Database: PDB / ID: 8xeo
TitleCrystal structure of MNT antitoxin
ComponentsMNT
KeywordsANTITOXIN / nucleotidyltransferase
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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 12, 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: MNT
B: MNT


Theoretical massNumber of molelcules
Total (without water)24,4542
Polymers24,4542
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-9 kcal/mol
Surface area10430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.169, 61.593, 66.483
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 MNT


Mass: 12226.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 6000, 0.1 M citric acid/sodium hydroxide, pH 4.0, 1M lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 11301 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 64.45 Å2 / CC1/2: 0.974 / Net I/σ(I): 22.3
Reflection shellResolution: 2.79→2.85 Å / Num. unique obs: 305 / CC1/2: 0.879

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4418refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→45.18 Å / SU ML: 0.4156 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.7378
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2739 1129 9.99 %
Rwork0.2152 10172 -
obs0.2211 11301 98.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.02 Å2
Refinement stepCycle: LAST / Resolution: 2.79→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 0 17 1593
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00261607
X-RAY DIFFRACTIONf_angle_d0.51292177
X-RAY DIFFRACTIONf_chiral_restr0.0378253
X-RAY DIFFRACTIONf_plane_restr0.0044272
X-RAY DIFFRACTIONf_dihedral_angle_d4.0641211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-2.920.36831430.29941229X-RAY DIFFRACTION93.84
2.92-3.070.39311320.28021256X-RAY DIFFRACTION97.95
3.07-3.260.33351500.26551270X-RAY DIFFRACTION98.61
3.26-3.510.29821390.23281283X-RAY DIFFRACTION99.03
3.52-3.870.2911350.22521301X-RAY DIFFRACTION99.24
3.87-4.430.29291380.18151284X-RAY DIFFRACTION99.72
4.43-5.580.23511410.18041281X-RAY DIFFRACTION99.44
5.58-45.180.22311510.21091268X-RAY DIFFRACTION99.09
Refinement TLS params.Method: refined / Origin x: 11.1072594248 Å / Origin y: 38.8912717123 Å / Origin z: 35.1413189933 Å
111213212223313233
T0.555940820076 Å2-0.0196767887764 Å20.0609372280451 Å2-0.560415502693 Å20.0184468952734 Å2--0.535697098212 Å2
L0.776691904612 °20.757785333885 °20.625798158162 °2-1.96793337591 °20.940621181936 °2--1.18524127859 °2
S-0.14425424515 Å °0.10109209259 Å °-0.0948241259127 Å °-0.175911836184 Å °0.167235103554 Å °-0.168466704525 Å °0.104963594619 Å °0.10557029803 Å °0.0184606298694 Å °
Refinement TLS groupSelection details: all

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