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- PDB-6epg: Structure of the epsilon_1 / zeta_1 antitoxin / toxin system from... -

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Basic information

Entry
Database: PDB / ID: 6epg
TitleStructure of the epsilon_1 / zeta_1 antitoxin / toxin system from Neisseria gonorrhoeae.
Components
  • Epsilon_1 antitoxin
  • Zeta_1 toxin
KeywordsTOXIN / bacterial toxin antitoxin systems / small molecule kinases / antitoxin
Function / homologyKfrB domain / KfrB protein / Zeta toxin domain / Zeta toxin / kinase activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Epsilon_1 antitoxin / Zeta_1 toxin
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRocker, A. / Meinhart, A.
CitationJournal: Nat Commun / Year: 2018
Title: The ng_ zeta 1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis.
Authors: Rocker, A. / Peschke, M. / Kittila, T. / Sakson, R. / Brieke, C. / Meinhart, A.
History
DepositionOct 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epsilon_1 antitoxin
B: Zeta_1 toxin
C: Epsilon_1 antitoxin
D: Zeta_1 toxin
E: Epsilon_1 antitoxin
F: Zeta_1 toxin
G: Epsilon_1 antitoxin
H: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,02330
Polymers209,9108
Non-polymers2,11322
Water1,982110
1
A: Epsilon_1 antitoxin
B: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0548
Polymers52,4772
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Epsilon_1 antitoxin
D: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9587
Polymers52,4772
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Epsilon_1 antitoxin
F: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0548
Polymers52,4772
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Epsilon_1 antitoxin
H: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9587
Polymers52,4772
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.760, 149.580, 125.090
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
12B
22D
32F
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 60
2115C1 - 60
3115E1 - 60
4115G1 - 60
1125B1 - 401
2125D1 - 401
3125F1 - 401
4125H1 - 401

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999655, -0.021362, -0.015287), (0.021233, -0.999738, 0.008528), (-0.015465, 0.0082, 0.999847)42.19691, 118.86759, -0.20918
3given(0.999687, -0.015654, 0.019492), (-0.014878, -0.999116, -0.039327), (0.02009, 0.039024, -0.999036)5.96319, 132.22984, 58.05952
4given(-0.999876, 0.002017, 0.015646), (0.001387, 0.999191, -0.040181), (-0.015714, -0.040155, -0.99907)33.68968, -7.75841, 63.72874

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Components

#1: Protein
Epsilon_1 antitoxin


Mass: 7377.974 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D5K9E3
#2: Protein
Zeta_1 toxin


Mass: 45099.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: K115A Walker A lysine to alanine mutation / Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: D5K9G7
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 3.54 Å3/Da / Density % sol: 65.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 100 mM sodium citrate pH 4.5, 1.8 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9797 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 108038 / % possible obs: 99.7 % / Redundancy: 13.9 % / CC1/2: 0.998 / Net I/σ(I): 11.8
Reflection shellResolution: 2.4→2.8 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 2.5 / CC1/2: 0.826 / Rrim(I) all: 0.152 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→48.91 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.792 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26956 5687 5 %RANDOM
Rwork0.2258 ---
obs0.22799 108038 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.81 Å2
2---2.69 Å2-0 Å2
3---2.61 Å2
Refinement stepCycle: 1 / Resolution: 2.4→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14071 0 110 110 14291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914330
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213455
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.97919240
X-RAY DIFFRACTIONr_angle_other_deg0.921331307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62551782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52725.08691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.574152616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.87715100
X-RAY DIFFRACTIONr_chiral_restr0.0740.22151
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022765
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9414.8367158
X-RAY DIFFRACTIONr_mcbond_other2.9354.8367157
X-RAY DIFFRACTIONr_mcangle_it4.5567.2458930
X-RAY DIFFRACTIONr_mcangle_other4.5577.2458931
X-RAY DIFFRACTIONr_scbond_it3.615.4197172
X-RAY DIFFRACTIONr_scbond_other3.5955.4057085
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.887.86610179
X-RAY DIFFRACTIONr_long_range_B_refined7.66855.91914802
X-RAY DIFFRACTIONr_long_range_B_other7.6655.91914788
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A321medium positional0.260.5
11C321medium positional0.260.5
11E321medium positional0.230.5
11G321medium positional0.190.5
22B2308medium positional0.160.5
22D2308medium positional0.150.5
22F2308medium positional0.130.5
22H2308medium positional0.160.5
11A566loose positional0.795
11C566loose positional0.565
11E566loose positional0.645
11G566loose positional0.575
22B3617loose positional0.445
22D3617loose positional0.445
22F3617loose positional0.455
22H3617loose positional0.445
11A321medium thermal3.922
11C321medium thermal4.452
11E321medium thermal8.822
11G321medium thermal6.322
22B2308medium thermal3.242
22D2308medium thermal2.492
22F2308medium thermal3.712
22H2308medium thermal2.942
11A566loose thermal4.6810
11C566loose thermal5.6210
11E566loose thermal10.4210
11G566loose thermal6.9710
22B3617loose thermal3.6510
22D3617loose thermal3.1510
22F3617loose thermal4.1710
22H3617loose thermal3.3110
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 420 -
Rwork0.331 7979 -
obs--99.72 %

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