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- PDB-6gw6: Structure of the Pseudomonas putida RES-Xre toxin-antitoxin complex -

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Basic information

Entry
Database: PDB / ID: 6gw6
TitleStructure of the Pseudomonas putida RES-Xre toxin-antitoxin complex
Components
  • RES toxin
  • Xre antitoxin
KeywordsTOXIN / Toxin antitoxin type II system / Xre / Cro repressor / RES domain / NAD+ glycohydrolase / NADase
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / nucleotidyltransferase activity / DNA binding
Similarity search - Function
Antitoxin Xre / Antitoxin Xre-like, helix-turn-helix domain / Antitoxin Xre-like helix-turn-helix domain / Antitoxin Xre/MbcA/ParS-like, toxin-binding domain / Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain / RES domain / RES domain / RES
Similarity search - Domain/homology
IMIDAZOLE / Antitoxin / RES family NAD+ phosphorylase / Toxin Res / Antitoxin Xre
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.205 Å
AuthorsSenissar, M. / Brodersen, D.E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Danish National Research FoundationDNRF120 Denmark
CitationJournal: Mol. Microbiol. / Year: 2019
Title: The RES domain toxins of RES-Xre toxin-antitoxin modules induce cell stasis by degrading NAD.
Authors: Skjerning, R.B. / Senissar, M. / Winther, K.S. / Gerdes, K. / Brodersen, D.E.
History
DepositionJun 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: 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.year / _citation_author.name
Revision 1.2Aug 26, 2020Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: RES toxin
B: Xre antitoxin
C: Xre antitoxin
D: RES toxin
E: Xre antitoxin
F: Xre antitoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,13610
Polymers99,8146
Non-polymers3224
Water1,69394
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14810 Å2
ΔGint-47 kcal/mol
Surface area37250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.060, 90.330, 186.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 1 through 6 or resid 8...
21(chain F and (resid 1 through 6 or resid 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain C and (resid 1 through 6 or resid 8...C1 - 6
121(chain C and (resid 1 through 6 or resid 8...C8 - 25
131(chain C and (resid 1 through 6 or resid 8...C0
141(chain C and (resid 1 through 6 or resid 8...C6
151(chain C and (resid 1 through 6 or resid 8...C1 - 149
161(chain C and (resid 1 through 6 or resid 8...C63 - 66
171(chain C and (resid 1 through 6 or resid 8...C114 - 146
181(chain C and (resid 1 through 6 or resid 8...C148
211(chain F and (resid 1 through 6 or resid 8...F1 - 6
221(chain F and (resid 1 through 6 or resid 8...F8 - 25
231(chain F and (resid 1 through 6 or resid 8...F27 - 44
241(chain F and (resid 1 through 6 or resid 8...F46 - 59
251(chain F and (resid 1 through 6 or resid 8...F63 - 66
261(chain F and (resid 1 through 6 or resid 8...F6 - 1102
271(chain F and (resid 1 through 6 or resid 8...F0
281(chain F and (resid 1 through 6 or resid 8...F1 - 149
291(chain F and (resid 1 through 6 or resid 8...F148

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Components

#1: Protein RES toxin


Mass: 15950.161 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_12385, B7H19_10550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179RGC3, UniProt: Q88K57*PLUS
#2: Protein
Xre antitoxin


Mass: 16978.436 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: AYO08_12380, B7H19_10555, CBL13_00496, CBP06_13110 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A179RFM7, UniProt: Q88K58*PLUS
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium malonate pH 6.0 and 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→45.165 Å / Num. obs: 51891 / % possible obs: 99.16 % / Redundancy: 13.5 % / Net I/σ(I): 12.25
Reflection shellResolution: 2.205→2.284 Å

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2.205→45.165 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.77
RfactorNum. reflection% reflection
Rfree0.2529 2483 4.81 %
Rwork0.2141 --
obs0.2159 51654 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 227.06 Å2 / Biso mean: 66.0127 Å2 / Biso min: 28.45 Å2
Refinement stepCycle: final / Resolution: 2.205→45.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7014 0 22 94 7130
Biso mean--104.74 56.09 -
Num. residues----886
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1221X-RAY DIFFRACTION12.395TORSIONAL
12F1221X-RAY DIFFRACTION12.395TORSIONAL
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)
10.8030.5512-0.25012.1161.49092.01710.139-0.0668-0.1037-0.1485-0.03580.224-0.2446-0.0016-0.16670.2931-0.0286-0.03580.36730.01880.382941.669434.44792.6559
21.08260.59580.98011.84120.6520.6780.08620.1819-0.1157-0.16850.0451-0.1485-0.06830.0169-0.16550.3213-0.0260.02870.3634-0.01730.429944.044436.996103.9298
39.6767-0.4954-1.36735.0437-1.25916.45360.5098-0.31730.25820.1099-0.24040.1775-1.11870.305-0.16510.5099-0.0180.02380.50510.00290.44346.788150.0141103.82
41.52070.4367-0.22949.2268-0.78651.15390.049-0.06830.1212-0.56150.06250.94110.1343-0.2329-0.21770.291-0.02630.02390.3748-0.06460.482634.227840.5047101.1032
53.645-0.35830.97820.48760.9611.3442-0.0155-0.4999-0.03490.0477-0.11010.23680.0363-0.12470.0880.3670.01490.00960.38380.00080.406449.234822.3816100.3126
65.33440.02171.24820.8541-0.18683.34670.22160.690.2001-0.1534-0.32080.14880.4959-0.09020.03260.38540.06410.05840.4807-0.03120.389352.401425.719690.2017
72.7955-0.28420.30131.2394-0.33442.7644-0.03330.16580.28270.1471-0.16950.18750.44040.17660.18990.3537-0.03510.01790.3421-0.03020.416345.804726.8978101.1321
87.3275-0.1001-1.00985.27111.3633.5340.2149-0.36210.81120.11830.1829-0.2544-0.05550.6187-0.20410.3397-0.03170.0220.4261-0.03980.454935.094224.01589.6098
91.0178-1.6659-1.46812.15461.81924.74060.4382-0.44650.3660.1991-0.83720.5428-0.4068-0.96590.29590.38910.0010.01660.43490.01390.450931.258442.4855106.652
101.0456-0.5935-0.81568.96391.46812.5536-0.35352.01470.0306-0.948-0.47540.4886-0.17720.06911.04550.80180.1026-0.04560.7507-0.13090.920539.82744.566781.908
114.00060.31080.17937.77970.04285.01330.33060.1870.4213-0.7659-0.08771.1312-0.0234-0.35080.05780.47460.0813-0.01280.62040.05090.5836.717654.903984.5092
128.38291.4368-0.95783.196-0.65633.54460.11081.1826-0.1102-0.4664-0.00570.2545-0.4653-0.4633-0.04230.63780.0759-0.10090.6927-0.00880.604642.128259.322373.3967
132.0044-0.2204-1.98112.11990.6614.01490.17380.01561.4287-0.2923-0.68530.474-1.6512-1.11770.65040.850.1161-0.08990.5494-0.13980.747846.664871.008883.6318
143.08140.30770.73042.82181.11754.16890.2379-0.10140.54010.7382-0.5665-0.1541-0.1427-0.07710.22960.7658-0.1756-0.00940.4889-0.02580.752254.962571.820783.7754
150.8019-0.0464-0.87713.0671-2.84323.22470.02540.2430.2653-0.0971-0.1154-0.1062-0.5182-0.09640.06430.6327-0.0817-0.07150.4739-0.00860.53448.504957.980184.9848
164.7921-0.7965-0.71642.87190.53434.14770.0583-0.41070.25240.3367-0.03790.1439-0.55430.0834-0.04540.434-0.04540.00040.3563-0.01870.420550.844253.73698.4428
174.13070.5446-0.24343.0949-0.52511.3863-0.36780.2312-0.2292-0.37760.167-0.2376-0.07970.16810.17190.4611-0.0280.00430.4398-0.02040.408551.386447.670690.383
183.2707-0.4322-0.80382.65610.75594.50330.4792-0.1654-0.42170.31660.27-1.51060.5497-0.7507-0.56920.83370.5976-0.16111.7085-0.31150.915453.695734.841780.3508
193.53970.750.46525.56371.28362.91080.1698-0.0445-0.1506-0.4629-0.1384-0.5295-0.29220.63590.0530.4078-0.01850.08540.62150.05770.564967.385643.179280.0969
203.83290.54540.32332.20061.99172.8046-0.07830.40060.3239-0.5510.1498-0.1154-0.19120.8982-0.06610.6807-0.0230.11330.72330.1060.483663.37751.126669.7255
214.49830.9602-0.36998.60990.02834.8512-0.20160.3702-0.1679-0.9106-0.0280.92170.2641-0.43540.22830.7375-0.03120.05690.63960.00580.453548.697141.875971.1712
222.1641-0.4922-1.06092.89620.14672.64730.1339-0.52190.20480.71860.1625-0.13-0.02790.0222-0.19380.6255-0.00590.0220.55240.0110.436445.000138.8717129.4273
230.9538-1.1456-0.06171.34190.33281.35330.0477-0.0873-0.04890.1069-0.0764-0.2812-0.11910.2879-0.00060.5101-0.03160.0290.4282-0.04240.427947.135642.1386116.4305
245.41710.7684-0.62695.30960.9074.29050.0777-0.6705-1.17710.3066-0.1774-0.56330.54790.30530.08960.37970.03980.01810.45330.02160.578353.090333.8524120.8502
253.112-0.8724-0.3831.0856-0.58052.07710.0291-0.0644-0.360.30540.11961.0709-0.0481-0.6408-0.09890.55-0.03870.15570.6580.01720.682130.036736.8653124.2784
266.1518-0.8485-0.37134.1569-0.76545.36510.2376-1.23590.37390.4804-0.59390.2073-0.6918-0.6166-0.06180.64370.05430.14580.8649-0.14970.515932.402843.6578132.4555
273.881-1.05921.23241.1727-0.45711.2032-0.2003-0.5151-0.50420.24810.19660.05840.0737-0.552-0.08510.5275-0.01790.12850.497-0.0050.513335.379536.0701122.5905
289.0125-1.4612-1.98944.7269-1.62043.0355-0.2204-1.5046-1.22391.39540.6066-0.5358-0.78460.8771-0.2041.057-0.03390.09580.8190.25830.612340.661828.7627135.9583
293.894-1.2583-1.21481.02971.75434.52740.2648-0.11620.08490.08530.16110.0086-0.19350.9492-0.47160.43410.0027-0.03450.5228-0.06260.594855.682631.0714115.4105
304.8712.43131.49833.24573.11263.18010.0613-0.38830.40740.0581.8063-2.07650.08050.4403-1.57080.7813-0.03060.01290.8496-0.07030.804158.436742.7638135.8596
312.949-0.68670.99524.6658-0.25633.29360.2059-0.22120.10810.0008-0.0284-0.3878-0.28060.1264-0.1090.6048-0.0613-0.07960.53170.01690.50266.836954.4742137.4711
320.68620.8590.31111.4404-0.23262.35980.0783-0.011-0.1152-0.8119-0.0044-0.12661.2926-0.4327-0.04641.1355-0.189-0.01690.76010.05240.635769.02665.8116124.3789
334.88081.4488-2.12473.480.0592.47951.1954-0.92170.75870.6387-0.4272-0.4579-1.04990.3678-0.68020.8889-0.1728-0.01870.7315-0.07270.825273.474775.557130.0885
343.2453.41580.73524.91422.35231.88010.1203-0.16140.31550.1106-0.40060.2192-0.5037-0.03230.16030.6673-0.0284-0.09580.46080.04960.477161.200559.0227129.6183
353.3295-0.5853-0.13423.96240.35984.0321-0.01950.03720.0804-0.298-0.0487-0.0103-0.57050.21910.06610.4798-0.0861-0.03030.4345-0.02220.440654.645854.913117.479
363.1674-0.2313-0.18723.9088-1.73652.8969-0.1171-0.11420.46290.5572-0.15380.0779-0.7468-0.43490.21640.68690.0386-0.05050.5083-0.06060.419250.443854.3871126.7003
374.38981.7745-0.01615.8586-0.37524.3933-0.0091-0.66960.53570.0490.25871.31650.8057-1.01550.08020.6063-0.02340.06380.7719-0.09510.662436.02459.0587138.4513
380.33811.24610.31165.7427-0.35872.34490.1317-0.1490.01380.4034-0.19630.37190.0987-0.15980.04770.58530.03650.06480.5381-0.07530.547745.094174.4011137.613
392.8105-1.00760.18872.9884-0.58822.8267-0.6479-1.36550.34261.50230.14540.1118-0.41620.29270.47360.97850.00350.02120.9096-0.19990.648549.956163.0148153.5595
404.49691.031-0.03474.7269-0.54353.417-0.1402-0.44610.14580.33970.06910.20090.31070.73850.02840.70480.02470.01080.6399-0.06530.532851.173457.5933146.332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )A1 - 31
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 48 )A32 - 48
3X-RAY DIFFRACTION3chain 'A' and (resid 49 through 55 )A49 - 55
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 66 )A56 - 66
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 86 )A67 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 100 )A87 - 100
7X-RAY DIFFRACTION7chain 'A' and (resid 101 through 121 )A101 - 121
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 130 )A122 - 130
9X-RAY DIFFRACTION9chain 'A' and (resid 131 through 145 )A131 - 145
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 6 )B1 - 6
11X-RAY DIFFRACTION11chain 'B' and (resid 7 through 22 )B7 - 22
12X-RAY DIFFRACTION12chain 'B' and (resid 23 through 39 )B23 - 39
13X-RAY DIFFRACTION13chain 'B' and (resid 40 through 51 )B40 - 51
14X-RAY DIFFRACTION14chain 'B' and (resid 52 through 80 )B52 - 80
15X-RAY DIFFRACTION15chain 'B' and (resid 81 through 101 )B81 - 101
16X-RAY DIFFRACTION16chain 'B' and (resid 102 through 122 )B102 - 122
17X-RAY DIFFRACTION17chain 'B' and (resid 123 through 149 )B123 - 149
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 8 )C1 - 8
19X-RAY DIFFRACTION19chain 'C' and (resid 9 through 51 )C9 - 51
20X-RAY DIFFRACTION20chain 'C' and (resid 52 through 129 )C52 - 129
21X-RAY DIFFRACTION21chain 'C' and (resid 130 through 149 )C130 - 149
22X-RAY DIFFRACTION22chain 'D' and (resid 1 through 31 )D1 - 31
23X-RAY DIFFRACTION23chain 'D' and (resid 32 through 55 )D32 - 55
24X-RAY DIFFRACTION24chain 'D' and (resid 56 through 66 )D56 - 66
25X-RAY DIFFRACTION25chain 'D' and (resid 67 through 86 )D67 - 86
26X-RAY DIFFRACTION26chain 'D' and (resid 87 through 100 )D87 - 100
27X-RAY DIFFRACTION27chain 'D' and (resid 101 through 121 )D101 - 121
28X-RAY DIFFRACTION28chain 'D' and (resid 122 through 130 )D122 - 130
29X-RAY DIFFRACTION29chain 'D' and (resid 131 through 145 )D131 - 145
30X-RAY DIFFRACTION30chain 'E' and (resid 1 through 9 )E1 - 9
31X-RAY DIFFRACTION31chain 'E' and (resid 10 through 39 )E10 - 39
32X-RAY DIFFRACTION32chain 'E' and (resid 40 through 65 )E40 - 65
33X-RAY DIFFRACTION33chain 'E' and (resid 66 through 80 )E66 - 80
34X-RAY DIFFRACTION34chain 'E' and (resid 81 through 101 )E81 - 101
35X-RAY DIFFRACTION35chain 'E' and (resid 102 through 122 )E102 - 122
36X-RAY DIFFRACTION36chain 'E' and (resid 123 through 149 )E123 - 149
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 29 )F1 - 29
38X-RAY DIFFRACTION38chain 'F' and (resid 30 through 101 )F30 - 101
39X-RAY DIFFRACTION39chain 'F' and (resid 102 through 122 )F102 - 122
40X-RAY DIFFRACTION40chain 'F' and (resid 123 through 149 )F123 - 149

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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