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- PDB-7ae9: Crystal structure of mono-AMPylated HEPN(R46E) toxin in complex w... -

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Basic information

Entry
Database: PDB / ID: 7ae9
TitleCrystal structure of mono-AMPylated HEPN(R46E) 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
bsu32300-like / : / Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / : / Ribonuclease HepT-like / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) ...bsu32300-like / : / Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / : / Ribonuclease HepT-like / Nucleotidyltransferase superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE / Protein adenylyltransferase MntA / tRNA nuclease HepT
Similarity search - Component
Biological speciesAphanizomenon flos-aquae 2012/KM1/D3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 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 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: MNT ANTITOXIN
F: MNT ANTITOXIN
G: MNT ANTITOXIN
H: MNT ANTITOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,71611
Polymers142,7718
Non-polymers9463
Water905
1
A: HEPN toxin
B: HEPN toxin
E: MNT ANTITOXIN
F: MNT ANTITOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0166
Polymers71,3854
Non-polymers6302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-40 kcal/mol
Surface area25270 Å2
MethodPISA
2
C: HEPN toxin
D: HEPN toxin
G: MNT ANTITOXIN
H: MNT ANTITOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7015
Polymers71,3854
Non-polymers3151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-36 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.250, 204.543, 73.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 13 or (resid 14...
21(chain B and (resid 3 through 13 or (resid 14...
31(chain C and (resid 3 through 13 or (resid 14...
41(chain D and ((resid 3 and (name N or name...
12(chain E and (resid 6 or (resid 7 through 14...
22(chain F and (resid 6 through 33 or (resid 34...
32(chain G and (resid 6 or (resid 7 through 14...
42(chain H and (resid 6 through 17 or (resid 18...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNLEULEU(chain A and (resid 3 through 13 or (resid 14...AA3 - 133 - 13
121GLUGLUGLUGLU(chain A and (resid 3 through 13 or (resid 14...AA1414
131ASNASNLEULEU(chain A and (resid 3 through 13 or (resid 14...AA3 - 1483 - 148
141ASNASNLEULEU(chain A and (resid 3 through 13 or (resid 14...AA3 - 1483 - 148
151ASNASNLEULEU(chain A and (resid 3 through 13 or (resid 14...AA3 - 1483 - 148
161ASNASNLEULEU(chain A and (resid 3 through 13 or (resid 14...AA3 - 1483 - 148
211ASNASNLEULEU(chain B and (resid 3 through 13 or (resid 14...BB3 - 133 - 13
221GLUGLUGLUGLU(chain B and (resid 3 through 13 or (resid 14...BB1414
231ASNASNGLUGLU(chain B and (resid 3 through 13 or (resid 14...BB3 - 1443 - 144
241ASNASNGLUGLU(chain B and (resid 3 through 13 or (resid 14...BB3 - 1443 - 144
251ASNASNGLUGLU(chain B and (resid 3 through 13 or (resid 14...BB3 - 1443 - 144
261ASNASNGLUGLU(chain B and (resid 3 through 13 or (resid 14...BB3 - 1443 - 144
311ASNASNLEULEU(chain C and (resid 3 through 13 or (resid 14...CC3 - 133 - 13
321GLUGLUGLUGLU(chain C and (resid 3 through 13 or (resid 14...CC1414
331THRTHRGLUGLU(chain C and (resid 3 through 13 or (resid 14...CC2 - 1452 - 145
341THRTHRGLUGLU(chain C and (resid 3 through 13 or (resid 14...CC2 - 1452 - 145
351THRTHRGLUGLU(chain C and (resid 3 through 13 or (resid 14...CC2 - 1452 - 145
361THRTHRGLUGLU(chain C and (resid 3 through 13 or (resid 14...CC2 - 1452 - 145
411ASNASNASNASN(chain D and ((resid 3 and (name N or name...DD33
421ASNASNGLUGLU(chain D and ((resid 3 and (name N or name...DD3 - 1443 - 144
431ASNASNGLUGLU(chain D and ((resid 3 and (name N or name...DD3 - 1443 - 144
441ASNASNGLUGLU(chain D and ((resid 3 and (name N or name...DD3 - 1443 - 144
451ASNASNGLUGLU(chain D and ((resid 3 and (name N or name...DD3 - 1443 - 144
112PROPROPROPRO(chain E and (resid 6 or (resid 7 through 14...EE66
122THRTHRLEULEU(chain E and (resid 6 or (resid 7 through 14...EE7 - 147 - 14
132LYSLYSVALVAL(chain E and (resid 6 or (resid 7 through 14...EE4 - 1504 - 150
142LYSLYSVALVAL(chain E and (resid 6 or (resid 7 through 14...EE4 - 1504 - 150
152LYSLYSVALVAL(chain E and (resid 6 or (resid 7 through 14...EE4 - 1504 - 150
212PROPROSERSER(chain F and (resid 6 through 33 or (resid 34...FF6 - 336 - 33
222ARGARGTHRTHR(chain F and (resid 6 through 33 or (resid 34...FF34 - 3634 - 36
232PROPROVALVAL(chain F and (resid 6 through 33 or (resid 34...FF6 - 1506 - 150
242PROPROVALVAL(chain F and (resid 6 through 33 or (resid 34...FF6 - 1506 - 150
252PROPROVALVAL(chain F and (resid 6 through 33 or (resid 34...FF6 - 1506 - 150
262PROPROVALVAL(chain F and (resid 6 through 33 or (resid 34...FF6 - 1506 - 150
312PROPROPROPRO(chain G and (resid 6 or (resid 7 through 14...GG66
322THRTHRLEULEU(chain G and (resid 6 or (resid 7 through 14...GG7 - 147 - 14
332LYSLYSVALVAL(chain G and (resid 6 or (resid 7 through 14...GG4 - 1504 - 150
342LYSLYSVALVAL(chain G and (resid 6 or (resid 7 through 14...GG4 - 1504 - 150
352LYSLYSVALVAL(chain G and (resid 6 or (resid 7 through 14...GG4 - 1504 - 150
362LYSLYSVALVAL(chain G and (resid 6 or (resid 7 through 14...GG4 - 1504 - 150
412PROPROARGARG(chain H and (resid 6 through 17 or (resid 18...HH6 - 176 - 17
422LEULEULYSLYS(chain H and (resid 6 through 17 or (resid 18...HH18 - 2118 - 21
432ILEILEVALVAL(chain H and (resid 6 through 17 or (resid 18...HH5 - 1505 - 150
442ILEILEVALVAL(chain H and (resid 6 through 17 or (resid 18...HH5 - 1505 - 150
452ILEILEVALVAL(chain H and (resid 6 through 17 or (resid 18...HH5 - 1505 - 150
462ILEILEVALVAL(chain H and (resid 6 through 17 or (resid 18...HH5 - 1505 - 150

NCS ensembles :
ID
1
2

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Components

#1: Protein
HEPN toxin


Mass: 18312.643 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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.: 4
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: Chemical ChemComp-2DA / 2',3'-DIDEOXYADENOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 315.222 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O5P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.66 Å3/Da / Density % sol: 53.7 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystallization buffer was 0,1M MOPS-HEPES pH 7.5, 9% PEG4K, 18% glycerol, 30 mM ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.9→204.543 Å / Num. obs: 34618 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 69.88 Å2 / Rpim(I) all: 0.037 / Rrim(I) all: 0.1 / Rsym value: 0.089 / Net I/av σ(I): 6.6 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs
2.9-3.067.60.71413770449800.2940.8130.7143
3.06-3.247.20.4411.63381446850.1870.5050.4414.5
3.24-3.477.70.2822.43421544410.1130.3170.2826.6
3.47-3.747.50.16343116141300.0660.1840.16310.1
3.74-4.17.20.0966.52753038300.040.1090.09614.1
4.1-4.597.60.0679.22670635020.0270.0750.06720
4.59-5.297.20.05710.82212330790.0240.0650.05720.6
5.29-6.487.50.05911.11976826390.0240.0670.05918.5
6.48-9.1770.03913.71455520930.0160.0440.03926.2
9.17-204.5436.40.03116.5790412390.0140.0350.03136.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.7 Å102.28 Å
Translation2.7 Å102.28 Å

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AE2

7ae2


Resolution: 2.9→102.271 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.07 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 6291 9.67 %
Rwork0.2033 58781 -
obs0.2075 34528 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.2 Å2 / Biso mean: 77.6231 Å2 / Biso min: 30.16 Å2
Refinement stepCycle: final / Resolution: 2.9→102.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8419 0 60 5 8484
Biso mean--93.14 55.4 -
Num. residues----1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058656
X-RAY DIFFRACTIONf_angle_d0.74911825
X-RAY DIFFRACTIONf_chiral_restr0.0471423
X-RAY DIFFRACTIONf_plane_restr0.0061504
X-RAY DIFFRACTIONf_dihedral_angle_d13.7845089
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2252X-RAY DIFFRACTION10.352TORSIONAL
12B2252X-RAY DIFFRACTION10.352TORSIONAL
13C2252X-RAY DIFFRACTION10.352TORSIONAL
14D2252X-RAY DIFFRACTION10.352TORSIONAL
21E2028X-RAY DIFFRACTION10.352TORSIONAL
22F2028X-RAY DIFFRACTION10.352TORSIONAL
23G2028X-RAY DIFFRACTION10.352TORSIONAL
24H2028X-RAY DIFFRACTION10.352TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.9-2.9330.38771910.34711977100
2.933-2.96750.30892020.32482001100
2.9675-3.00370.34722140.31351897100
3.0037-3.04170.35292470.30531950100
3.0417-3.08170.32541840.28831989100
3.0817-3.12390.34241760.26852001100
3.1239-3.16860.30811890.24251984100
3.1686-3.21590.27142020.2296190999
3.2159-3.26610.28262290.24331987100
3.2661-3.31970.3161940.24451945100
3.3197-3.37690.28551980.24892004100
3.3769-3.43830.26471920.23121937100
3.4383-3.50450.29652330.22881958100
3.5045-3.5760.28592070.22721949100
3.576-3.65380.26281880.22091998100
3.6538-3.73880.22561980.18531942100
3.7388-3.83230.26642190.17941941100
3.8323-3.93590.23842210.18761958100
3.9359-4.05170.23851960.1792005100
4.0517-4.18250.24622120.17551928100
4.1825-4.3320.22922380.16751957100
4.332-4.50540.20312040.16871936100
4.5054-4.71050.2231870.1631993100
4.7105-4.95880.21362480.17871934100
4.9588-5.26950.24012070.18811965100
5.2695-5.67630.27992230.20691961100
5.6763-6.24750.25932200.21991930100
6.2475-7.15130.2372340.20261940100
7.1513-9.0090.18642210.16841966100
9.009-102.2710.19762170.19551939100
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)
13.40810.71310.71162.3498-0.22691.7310.21250.08860.1885-0.0188-0.2124-0.0442-0.3246-0.05760.02990.36910.14150.02060.668-0.01320.462239.5958.6097.1856
23.2105-0.15170.8022.77740.53423.1559-0.0478-0.27960.27390.0502-0.1111-0.1485-0.24430.10420.17590.28490.03330.02370.45570.03180.464313.00858.8049-6.1195
33.23910.0892-0.13413.4395-0.7133.45740.0009-0.0832-0.18160.16370.1057-0.02570.4152-0.2532-0.1010.3496-0.0749-0.04210.34530.0370.4408-10.309792.708227.3534
42.60.49960.2113.06720.70063.53640.187-0.1016-0.10860.1257-0.00920.03270.643-0.7522-0.14590.6622-0.0208-0.02680.83420.02670.6176-32.960484.709738.0756
52.6615-0.92140.2561.4930.29411.6624-0.1224-0.34460.01630.15430.00990.1339-0.2746-0.25380.03990.4580.03420.03480.660.02770.471219.813166.868318.7796
61.92791.21140.51341.3395-0.89592.6985-0.37610.4860.20620.05840.1865-0.0456-0.59310.48960.17160.62250.05980.0050.9013-0.06890.586932.621566.0402-18.6263
71.43672.24640.10673.64640.01220.202-0.29570.52940.1941-0.15740.47140.21110.0917-0.2659-0.13110.5481-0.14220.01840.72820.03560.5233-25.779677.922614.5125
83.2821-0.5418-0.33631.39440.40651.94110.5336-0.2137-0.02030.2318-0.2614-0.21960.53930.1631-0.31680.9655-0.0081-0.05550.72620.08260.5791-12.919284.135951.9817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 148
2X-RAY DIFFRACTION2chain BB3 - 144
3X-RAY DIFFRACTION3chain CC2 - 145
4X-RAY DIFFRACTION4chain DD3 - 144
5X-RAY DIFFRACTION5chain EE4 - 150
6X-RAY DIFFRACTION6chain FF6 - 150
7X-RAY DIFFRACTION7chain GG4 - 150
8X-RAY DIFFRACTION8chain HH5 - 150

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