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- PDB-7ae2: Crystal structure of HEPN(H107A-Y109F) toxin in complex with MNT ... -

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Basic information

Entry
Database: PDB / ID: 7ae2
TitleCrystal structure of HEPN(H107A-Y109F) toxin in complex with MNT antitoxin
Components
  • HEPN toxin
  • MNT ANTITOXIN
KeywordsTOXIN/ANTITOXIN / toxin-antitoxin system / MNT-HEPN / AMPylation / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


protein adenylyltransferase / toxin-antitoxin complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / nucleotidyltransferase activity / endonuclease activity / nucleotide binding / ATP binding / metal ion binding
Similarity search - Function
Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / Ribonuclease HepT-like / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Protein adenylyltransferase MntA / tRNA nuclease HepT
Similarity search - Component
Biological speciesAphanizomenon flos-aquae 2012/KM1/D3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTamulaitiene, G. / Sasnauskas, G. / Songailiene, I. / Juozapaitis, J. / Siksnys, V.
CitationJournal: Mol.Cell / Year: 2020
Title: HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation.
Authors: Songailiene, I. / Juozapaitis, J. / Tamulaitiene, G. / Ruksenaite, A. / Sulcius, S. / Sasnauskas, G. / Venclovas, C. / Siksnys, V.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEPN toxin
B: MNT ANTITOXIN


Theoretical massNumber of molelcules
Total (without water)35,6382
Polymers35,6382
Non-polymers00
Water1,18966
1
A: HEPN toxin
B: MNT ANTITOXIN

A: HEPN toxin
B: MNT ANTITOXIN


Theoretical massNumber of molelcules
Total (without water)71,2754
Polymers71,2754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area8000 Å2
ΔGint-40 kcal/mol
Surface area24550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.709, 85.989, 100.105
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-233-

HOH

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Components

#1: Protein HEPN toxin


Mass: 18257.652 Da / Num. of mol.: 1 / Mutation: H107A Y109F
Source method: isolated from a genetically manipulated source
Details: C-terminal His-tag
Source: (gene. exp.) Aphanizomenon flos-aquae 2012/KM1/D3 (bacteria)
Gene: OA07_26455 / Plasmid: pACYC-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A0B0QJR1
#2: Protein MNT ANTITOXIN


Mass: 17380.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanizomenon flos-aquae 2012/KM1/D3 (bacteria)
Gene: OA07_26450 / Plasmid: pACYC-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A0B0QJN8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization buffer was 0,1 M MES-imidazole pH 6.5, 10% PEG 20K, 20% PEG550MME, 30 mM NaNO3, 30 mM Na2HPO4, 30 mM(NH4)2SO4

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)11.3862
SYNCHROTRONPETRA III, EMBL c/o DESY P13 (MX1)20.9796
Detector
TypeIDDetectorDate
PSI PILATUS 6M1PIXELMay 17, 2018
PSI PILATUS 6M2PIXELNov 24, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.38621
20.97961
ReflectionResolution: 2→55.521 Å / Num. all: 21539 / Num. obs: 21539 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 41.17 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Rsym value: 0.041 / Net I/av σ(I): 8.5 / Net I/σ(I): 22.3 / Num. measured all: 136995
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.116.50.4581.51995530810.2060.5290.4584.599.9
2.11-2.246.10.2492.71805829480.1150.2870.2497.699.8
2.24-2.396.60.1444.71825627830.0650.1660.14412.3100
2.39-2.586.30.0957.21610725620.0440.110.09516.5100
2.58-2.836.30.06210.51494623800.0280.0720.06222.499.7
2.83-3.166.60.04613.51429921820.0210.0540.04630.4100
3.16-3.656.40.03516.21220019140.0160.0410.03538.799.8
3.65-4.476.60.03217.61083816400.0140.0370.03247.2100
4.47-6.326.30.0318.1814212990.0140.0360.0347.399.9
6.32-55.5215.60.03514.841947500.0180.0420.03546.399.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
SCALA3.3.20data scaling
SHELXDEphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→50.053 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.26 / Phase error: 24.07 / Stereochemistry target values: ML
Details: Dataset 1 (17-MAY-18) is the primary dataset used for refinement. Dataset 2 (24-NOV-18), Se-Met SAD, was used for phasing.
RfactorNum. reflection% reflection
Rfree0.2266 4098 10.05 %
Rwork0.1992 36688 -
obs0.2019 21501 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.55 Å2 / Biso mean: 58.0177 Å2 / Biso min: 21.78 Å2
Refinement stepCycle: final / Resolution: 2→50.053 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2184 0 0 68 2252
Biso mean---61.88 -
Num. residues----281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022263
X-RAY DIFFRACTIONf_angle_d0.4373087
X-RAY DIFFRACTIONf_chiral_restr0.038364
X-RAY DIFFRACTIONf_plane_restr0.003401
X-RAY DIFFRACTIONf_dihedral_angle_d11.941364
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02350.31891410.29751264100
2.0235-2.04820.3571570.30741226100
2.0482-2.07420.32211390.28561290100
2.0742-2.10140.31891560.26171241100
2.1014-2.13020.3071640.25771252100
2.1302-2.16070.27231670.24081255100
2.1607-2.19290.19581200.2304123999
2.1929-2.22720.32841500.2431123398
2.2272-2.26370.27061220.22941306100
2.2637-2.30270.26181360.21881269100
2.3027-2.34460.27121380.22391315100
2.3446-2.38970.24031680.21291237100
2.3897-2.43850.23041390.22621274100
2.4385-2.49150.23671200.21841252100
2.4915-2.54950.29331210.22251295100
2.5495-2.61320.18621610.2272121597
2.6132-2.68390.21051390.20471288100
2.6839-2.76280.26771460.22411224100
2.7628-2.8520.26921650.21631280100
2.852-2.95390.25251320.231279100
2.9539-3.07220.26351080.21931300100
3.0722-3.2120.19291530.21251247100
3.212-3.38130.25691520.2147124299
3.3813-3.59310.19491330.19981303100
3.5931-3.87040.2021220.16291274100
3.8704-4.25970.17341420.15571283100
4.2597-4.87560.14761090.15871282100
4.8756-6.1410.24351520.19381276100
6.141-50.0530.24031460.1891124799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.72360.07741.16153.26340.49733.95080.0209-0.3192-0.26810.2549-0.1177-0.09390.1965-0.00420.10850.31810.0512-0.00940.2850.08120.2435-6.7943-5.986713.79
25.14350.11031.29014.04060.31284.7323-0.04460.0599-0.37490.26370.113-0.42950.17650.6081-0.08840.31550.06740.00760.34150.02330.3035-3.1897-5.450710.7497
34.40940.53110.64255.2141-1.06983.3251-0.1277-0.264-0.059-0.0690.0981-0.36710.129-0.21510.03810.5656-0.070.03110.65180.03790.6135-13.0363-17.91939.1709
40.71370.44280.41470.8339-0.78982.84850.1006-0.3668-0.1760.17260.1280.36920.0277-0.8397-0.18320.40450.03860.09930.64540.11850.5186-25.0737-9.036823.9002
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:93)A3 - 93
2X-RAY DIFFRACTION2(chain A and resid 94:144)A94 - 144
3X-RAY DIFFRACTION3(chain B and resid 4:92)B4 - 92
4X-RAY DIFFRACTION4(chain B and resid 93:150)B93 - 150

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