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- PDB-7ae6: Crystal structure of di-AMPylated HEPN(R102A) toxin -

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Basic information

Entry
Database: PDB / ID: 7ae6
TitleCrystal structure of di-AMPylated HEPN(R102A) toxin
ComponentsHEPN toxin
KeywordsTOXIN / toxin-antitoxin system / MNT-HEPN / AMPylation
Function / homology
Function and homology information


toxin-antitoxin complex / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA nuclease activity / endonuclease activity / nucleotide binding
Similarity search - Function
Ribonuclease HepT-like / tRNA nuclease HepT-like superfamily / : / Ribonuclease HepT-like
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / tRNA nuclease HepT
Similarity search - Component
Biological speciesAphanizomenon flos-aquae 2012/KM1/D3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,27112
Polymers36,5092
Non-polymers1,76110
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint12 kcal/mol
Surface area14230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.443, 62.722, 84.356
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HEPN toxin / HEPN toxin


Mass: 18254.605 Da / Num. of mol.: 2 / Mutation: R102A
Source method: isolated from a genetically manipulated source
Details: HEPN toxin
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: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 43.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 21.25% Ethylene glycol, 15% glycerol

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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: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→84.356 Å / Num. obs: 38600 / % possible obs: 98.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 27.94 Å2 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.018 / Rrim(I) all: 0.038 / Rsym value: 0.03 / Net I/av σ(I): 8.2 / Net I/σ(I): 18.9
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
1.65-1.743.70.4881.52105256250.3140.6370.4882.399.8
1.74-1.843.60.2672.71896353140.1760.3510.267499
1.84-1.973.80.1684.31902349990.1040.2150.1686.899.7
1.97-2.133.70.097.81748746860.0550.1130.0912.199.4
2.13-2.333.70.05511.91569342730.0340.070.05519.598.4
2.33-2.613.80.0416.71482338820.0240.050.0426.398.9
2.61-3.013.70.02822.81265734000.0170.0360.02833.497
3.01-3.693.90.02228.11124829080.0130.0270.02244.597.8
3.69-5.223.70.01833.4832522290.0110.0230.0185195.4
5.22-84.3563.50.02410.3455012840.0150.030.0245094.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å42.18 Å
Translation3 Å42.18 Å

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
SCALA3.2.19data scaling
MOLREP6phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AE2

7ae2


Resolution: 1.65→42.178 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2001 7121 10.05 %
Rwork0.1705 63742 -
obs0.1734 38541 95.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.68 Å2 / Biso mean: 35.4952 Å2 / Biso min: 17.54 Å2
Refinement stepCycle: final / Resolution: 1.65→42.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2309 0 112 121 2542
Biso mean--36.36 43.58 -
Num. residues----290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062590
X-RAY DIFFRACTIONf_angle_d0.8823545
X-RAY DIFFRACTIONf_chiral_restr0.048412
X-RAY DIFFRACTIONf_plane_restr0.005447
X-RAY DIFFRACTIONf_dihedral_angle_d12.0741549
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.66880.29952270.2787217097
1.6688-1.68840.29172670.2654214097
1.6884-1.7090.3072450.2623220297
1.709-1.73060.32822550.2582219298
1.7306-1.75340.28622550.2481211997
1.7534-1.77740.26922460.2362216896
1.7774-1.80280.28062160.2364209595
1.8028-1.82970.24612270.2262213494
1.8297-1.85830.21042360.204211194
1.8583-1.88880.24132100.2133226398
1.8888-1.92130.25282500.203215398
1.9213-1.95630.23562540.193221698
1.9563-1.99390.22482520.1851208797
1.9939-2.03460.19932500.1859218996
2.0346-2.07880.20012580.163215097
2.0788-2.12720.2292400.1705212296
2.1272-2.18040.1882570.1608205494
2.1804-2.23930.2152540.1665204191
2.2393-2.30520.17842090.1662217398
2.3052-2.37960.17772470.1628214096
2.3796-2.46470.20252650.1584214196
2.4647-2.56330.18432030.1556214595
2.5633-2.680.2062660.1665205994
2.68-2.82120.21132240.1619207692
2.8212-2.9980.19312120.1687204791
2.998-3.22940.18842230.1572213995
3.2294-3.55420.17872120.1514211594
3.5542-4.06810.16142240.1468203291
4.0681-5.1240.18792040.1583205791
5.124-42.1780.20532330.186201290
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)
14.46311.1764-1.12721.9847-0.92662.41770.0314-0.2149-0.212-0.0303-0.0612-0.03940.12850.01330.02660.29260.018-0.00350.17980.03510.201946.70357.078211.5609
22.24380.92340.60142.75970.59751.1382-0.01920.05260.1889-0.0580.00520.016-0.09680.07870.02060.1896-0.0060.00810.22720.01960.160555.325779.9533-2.3115
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 149
2X-RAY DIFFRACTION2chain BB4 - 147

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