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

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Basic information

Entry
Database: PDB / ID: 6epi
TitleStructure of the epsilon_1 / zeta_1 antitoxin / toxin system from Neisseria gonorrhoeae in complex with UNAM-4P.
Components
  • Epsilon_1 antitoxin
  • Zeta_1 toxin
KeywordsTOXIN / bacterial toxin antitoxin systems / small molecule kinases
Function / homologyKfrB domain / KfrB protein / P-loop containing nucleoside triphosphate hydrolase / ATP binding / UDP-N-acetyl-muramic acid-4'phosphate / CITRATE ANION / Epsilon_1 antitoxin / Zeta_1 toxin
Function and homology information
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_CC_half
Revision 1.3Jan 17, 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

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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)212,27527
Polymers207,7048
Non-polymers4,57219
Water2,540141
1
A: Epsilon_1 antitoxin
B: Zeta_1 toxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9736
Polymers51,9262
Non-polymers1,0484
Water181
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)53,2598
Polymers51,9262
Non-polymers1,3336
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)52,9736
Polymers51,9262
Non-polymers1,0484
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)53,0707
Polymers51,9262
Non-polymers1,1445
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.510, 149.320, 125.440
Angle α, β, γ (deg.)90.00, 94.36, 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 - 601
2115C1 - 601
3115E1 - 601
4115G1 - 601
1125B1 - 401
2125D1 - 401
3125F1 - 401
4125H1 - 401

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999617, -0.024404, -0.013068), (0.024264, -0.999648, 0.010765), (-0.013326, 0.010443, 0.999857)42.89608, 117.883118, -0.51717
3given(0.999209, -0.03359, 0.021305), (-0.033096, -0.999185, -0.023105), (0.022063, 0.022382, -0.999506)7.45503, 130.828827, 60.105099
4given(-0.999588, -0.002874, 0.028546), (-0.003706, 0.999569, -0.029123), (-0.02845, -0.029217, -0.999168)34.100571, -8.00758, 63.637539
5given(1), (1), (1)
6given(-0.99997, -0.006716, 0.003874), (0.00677, -0.999878, 0.014075), (0.003779, 0.014101, 0.999893)40.962002, 118.06665, -0.8984
7given(0.999963, -0.008432, -0.001506), (-0.008475, -0.999468, -0.031492), (-0.00124, 0.031504, -0.999503)5.95585, 130.565933, 59.84288
8given(-0.99983, -0.012082, 0.013949), (-0.012413, 0.999636, -0.023958), (-0.013655, -0.024127, -0.999616)35.17395, -8.32749, 63.512779

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
Epsilon_1 antitoxin


Mass: 7190.395 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: 44735.484 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: D5K9G7

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Non-polymers , 4 types, 160 molecules

#3: Chemical
ChemComp-BNW / UDP-N-acetyl-muramic acid-4'phosphate


Mass: 759.396 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H32N3O22P3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 68024 / % possible obs: 99.7 % / Redundancy: 4.1 % / CC1/2: 0.997 / Rrim(I) all: 0.113 / Net I/σ(I): 11.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / CC1/2: 0.744 / Rrim(I) all: 0.92 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EPG

6epg


Resolution: 2.8→49.17 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.749 / ESU R Free: 0.322 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24359 3688 5.1 %RANDOM
Rwork0.21909 ---
obs0.22043 68024 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 61.801 Å2
Baniso -1Baniso -2Baniso -3
1--2.36 Å20 Å21.04 Å2
2---2.46 Å20 Å2
3---4.6 Å2
Refinement stepCycle: 1 / Resolution: 2.8→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14055 0 275 141 14471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01914495
X-RAY DIFFRACTIONr_bond_other_d00.0213988
X-RAY DIFFRACTIONr_angle_refined_deg1.1321.96619489
X-RAY DIFFRACTIONr_angle_other_deg3.6922.98732235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.07451781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62824.878695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.761152764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.36915100
X-RAY DIFFRACTIONr_chiral_restr0.0760.22140
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216299
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023201
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_it2.056.0557148
X-RAY DIFFRACTIONr_mcbond_other2.056.0557147
X-RAY DIFFRACTIONr_mcangle_it3.5579.088921
X-RAY DIFFRACTIONr_mcangle_other3.5579.088922
X-RAY DIFFRACTIONr_scbond_it2.0566.3687347
X-RAY DIFFRACTIONr_scbond_other2.0546.3677345
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6339.40210568
X-RAY DIFFRACTIONr_long_range_B_refined5.92269.19115090
X-RAY DIFFRACTIONr_long_range_B_other5.92169.19615091
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
11A309MEDIUM POSITIONAL0.140.5
12C309MEDIUM POSITIONAL0.180.5
13E309MEDIUM POSITIONAL0.220.5
14G309MEDIUM POSITIONAL0.140.5
11A554LOOSE POSITIONAL0.395
12C554LOOSE POSITIONAL0.415
13E554LOOSE POSITIONAL0.495
14G554LOOSE POSITIONAL0.525
11A309MEDIUM THERMAL4.812
12C309MEDIUM THERMAL8.62
13E309MEDIUM THERMAL14.422
14G309MEDIUM THERMAL7.352
11A554LOOSE THERMAL4.7610
12C554LOOSE THERMAL8.9710
13E554LOOSE THERMAL15.310
14G554LOOSE THERMAL7.9410
21B2331MEDIUM POSITIONAL0.120.5
22D2331MEDIUM POSITIONAL0.110.5
23F2331MEDIUM POSITIONAL0.160.5
24H2331MEDIUM POSITIONAL0.160.5
21B3767LOOSE POSITIONAL0.355
22D3767LOOSE POSITIONAL0.355
23F3767LOOSE POSITIONAL0.45
24H3767LOOSE POSITIONAL0.395
21B2331MEDIUM THERMAL2.992
22D2331MEDIUM THERMAL2.932
23F2331MEDIUM THERMAL4.782
24H2331MEDIUM THERMAL4.612
21B3767LOOSE THERMAL3.3110
22D3767LOOSE THERMAL3.5810
23F3767LOOSE THERMAL5.1710
24H3767LOOSE THERMAL4.9610
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 225 -
Rwork0.397 4433 -
obs--86.63 %

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