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- PDB-6en0: Structure of the Tn1549 transposon Integrase (aa 82-397) in compl... -

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Basic information

Entry
Database: PDB / ID: 6en0
TitleStructure of the Tn1549 transposon Integrase (aa 82-397) in complex with circular intermediate DNA (CI5-DNA)
Components
  • (DNA (44-MER)) x 2
  • Int protein
KeywordsRECOMBINATION / transposase protein - DNA complex / tyrosine recombinase / Y-transposase / Tn916-like conjugative transposon / antibiotic resistance transfer
Function / homology
Function and homology information


integrase activity / DNA recombination / DNA binding
Similarity search - Function
Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily ...Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Int protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
Clostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRubio-Cosials, A. / Barabas, O.
CitationJournal: Cell / Year: 2018
Title: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.
Authors: Rubio-Cosials, A. / Schulz, E.C. / Lambertsen, L. / Smyshlyaev, G. / Rojas-Cordova, C. / Forslund, K. / Karaca, E. / Bebel, A. / Bork, P. / Barabas, O.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 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: Int protein
C: DNA (44-MER)
E: DNA (44-MER)
B: Int protein


Theoretical massNumber of molelcules
Total (without water)99,6514
Polymers99,6514
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14350 Å2
ΔGint-122 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 124.320, 77.400
Angle α, β, γ (deg.)90.00, 117.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Int protein / Integrase


Mass: 36286.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: int / Plasmid: pETM28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q7BP35
#2: DNA chain DNA (44-MER)


Mass: 13607.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Clostridioides difficile (bacteria)
#3: DNA chain DNA (44-MER)


Mass: 13469.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Clostridioides difficile (bacteria)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na Acetate pH4.6, 30% PEG300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.8→46.044 Å / Num. obs: 31128 / % possible obs: 96.6 % / Redundancy: 2.85 % / CC1/2: 0.995 / Rrim(I) all: 0.125 / Rsym value: 0.102 / Net I/σ(I): 10.67
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 2.87 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 2363 / CC1/2: 0.622 / Rrim(I) all: 1.739 / Rsym value: 1.415 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASERphasing
XDSdata scaling
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EMZ

6emz


Resolution: 2.8→46.044 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.15
RfactorNum. reflection% reflection
Rfree0.2543 1625 5.22 %
Rwork0.2268 --
obs0.2283 31128 96.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→46.044 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4502 1355 0 60 5917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036112
X-RAY DIFFRACTIONf_angle_d0.5798584
X-RAY DIFFRACTIONf_dihedral_angle_d20.972219
X-RAY DIFFRACTIONf_chiral_restr0.023971
X-RAY DIFFRACTIONf_plane_restr0.003888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.89130.39771350.40812764X-RAY DIFFRACTION94
2.8913-2.99450.40631550.37442709X-RAY DIFFRACTION93
2.9945-3.11430.31591380.34012707X-RAY DIFFRACTION94
3.1143-3.2560.3351400.30172673X-RAY DIFFRACTION92
3.256-3.42750.34161460.27362640X-RAY DIFFRACTION91
3.4275-3.6420.2941290.26442641X-RAY DIFFRACTION91
3.642-3.92270.3541370.26672634X-RAY DIFFRACTION90
3.9227-4.31670.27621430.23092706X-RAY DIFFRACTION92
4.3167-4.93960.20951310.19042652X-RAY DIFFRACTION92
4.9396-6.21670.2411590.18382703X-RAY DIFFRACTION92
6.2167-33.17520.1741570.17252692X-RAY DIFFRACTION90
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)
13.92011.1012.32722.5407-1.11072.67050.0442-0.1630.04660.7427-0.140.16140.5349-0.02510.37930.8701-0.10690.1860.6979-0.11140.665441.1572-23.902743.1722
21.3574-0.13630.44212.5383-2.01712.7854-0.2710.00850.19160.1129-0.05350.2735-0.44660.610.70390.5502-0.0818-0.02510.4562-0.12260.767546.8258-15.445235.011
33.3790.42452.51681.707-0.67272.5547-0.2786-0.33190.35690.16490.22670.5961-1.00840.0903-0.29950.66670.06860.07870.4425-0.140.806936.8607-10.964233.2367
43.2612-0.10711.83992.2089-0.62690.7478-0.6780.223-0.3697-0.4846-0.0057-0.33070.4056-0.3930.21670.91760.01930.20070.4282-0.01980.914225.0639-30.46915.3588
56.30210.81172.01322.81182.29932.2932-0.45430.23020.20510.5794-0.20250.6002-0.3852-0.07950.28920.6887-0.01470.210.34010.13920.836426.2977-35.046219.5159
62.3145-0.58340.7571.916-2.31145.27920.00090.12340.0627-1.1094-0.31350.21870.8874-0.47440.29231.0859-0.0584-0.11930.34220.05570.862523.9997-41.35676.6491
70.83370.4821-1.593-0.09590.44287.1324-0.7371-0.5034-0.5671-1.24450.0548-0.72692.19140.09020.47621.0523-0.14650.18490.5488-0.03540.974931.5896-41.944613.4574
83.60410.0588-1.992.0523-1.32144.08810.15290.27341.5498-0.41040.1021-0.4827-0.341-0.0064-0.06210.65160.05920.05660.48440.10340.939232.2093-21.02266.3436
91.5399-1.7143-1.18251.47070.57231.66470.86950.20220.0264-3.3549-0.21660.00311.3036-0.04-0.39261.2535-0.1577-0.04690.7602-0.25091.067713.7485-11.073616.7167
100.63741.6212-0.83334.86020.24011.92350.32080.22990.3898-0.5853-0.61780.35-0.21170.42450.28870.66330.21280.0620.66950.16640.919448.0563-30.567510.0648
111.6556-2.4845-3.44581.32011.74763.0828-0.47870.5832-0.27440.77550.54741.1745-0.2256-0.9029-0.36910.92540.0190.42460.8943-0.05751.543624.9729-15.004232.1417
122.57951.5073-0.48813.1171.76630.5597-0.5806-0.17880.4193-0.3943-0.21990.356-0.0029-0.22920.91041.07390.0740.24460.6582-0.02111.0481-10.28527.052645.0225
131.95992.71962.65663.24272.49232.16490.6205-0.23060.60650.1963-0.96150.8190.7497-0.21340.22491.07420.11190.39070.57260.0221.1098-9.55527.944246.5046
145.8516-5.8305-4.72244.44983.1653-0.50750.6435-0.30630.8989-0.4228-0.1926-0.5427-0.53090.1081-0.44290.89690.02890.15780.706-0.13711.015820.2035-13.037935.3363
152.9996-1.44572.09392.08130.31121.30030.83981.7619-0.5705-0.7778-0.3927-1.9582-0.15490.2521-0.59770.72080.11010.22310.784-0.05911.601848.0601-30.204110.8901
164.1804-0.23362.75970.5097-0.59371.5318-0.1358-0.4502-0.32390.8483-0.2819-1.2704-1.39380.0944-0.66610.96470.05370.23020.61350.04781.196218.94410.62755.8546
173.7911-1.37991.29825.84211.89023.75320.3784-0.92160.12610.2138-0.4379-1.09920.07660.1773-0.15290.76320.08140.10440.67960.24270.867111.1331-2.683557.1889
181.46890.03720.78690.68081.58645.84680.8308-0.82-0.96640.6178-1.3549-0.68382.9138-0.6198-0.48340.83120.1493-0.06420.23550.39532.01115.5614-13.951456.1758
193.32380.84153.26051.21481.24914.5247-0.0935-0.4453-1.3327-0.73970.0058-1.54480.8720.5556-0.32670.88280.13850.13180.58230.11741.414116.2515-12.131650.4685
201.60961.59591.58141.3833-0.17245.16560.02230.5685-0.9591-1.4037-0.16570.09671.2226-0.17570.36370.9762-0.00720.13410.6577-0.04020.9456-10.6382-6.163929.3161
213.47012.0597-0.57535.06783.51144.91510.02980.34830.0136-1.24650.4009-0.0818-1.0888-0.3004-0.38640.85610.05190.0220.44120.11360.4831-4.644110.238224.98
220.0006-0.1791.80015.46593.46413.7050.30690.2163-0.18750.05560.1832-0.37130.28790.4664-0.97130.6990.10370.14580.50870.08480.77176.983511.539730.8142
232.61442.81890.04115.6621.13412.01340.84960.81290.0185-1.65520.2228-0.9729-1.4491-0.5257-0.03531.31850.05010.32030.3075-0.29640.9479-5.988217.918324.5018
241.1009-1.0376-0.63834.62161.98643.21730.28890.168-0.0223-0.3227-0.27430.0699-0.3723-0.35150.04290.66-0.07050.03680.3582-0.07670.6245-7.24954.21431.7828
253.5584-1.8271-1.27135.27752.01233.1080.4354-0.1203-0.2787-0.06730.14410.5875-0.48590.169-0.63430.5550.01490.08060.6045-0.25810.94428.2723-12.492318.3035
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 99 )
2X-RAY DIFFRACTION2chain 'A' and (resid 100 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 192 )
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 242 )
5X-RAY DIFFRACTION5chain 'A' and (resid 243 through 275 )
6X-RAY DIFFRACTION6chain 'A' and (resid 276 through 297 )
7X-RAY DIFFRACTION7chain 'A' and (resid 298 through 314 )
8X-RAY DIFFRACTION8chain 'A' and (resid 315 through 356 )
9X-RAY DIFFRACTION9chain 'A' and (resid 357 through 394 )
10X-RAY DIFFRACTION10chain 'C' and (resid -15 through -5 )
11X-RAY DIFFRACTION11chain 'C' and (resid -4 through 5 )
12X-RAY DIFFRACTION12chain 'C' and (resid 6 through 20 )
13X-RAY DIFFRACTION13chain 'E' and (resid -13 through -5 )
14X-RAY DIFFRACTION14chain 'E' and (resid -4 through 8 )
15X-RAY DIFFRACTION15chain 'E' and (resid 9 through 18 )
16X-RAY DIFFRACTION16chain 'B' and (resid 82 through 99 )
17X-RAY DIFFRACTION17chain 'B' and (resid 100 through 128 )
18X-RAY DIFFRACTION18chain 'B' and (resid 129 through 144 )
19X-RAY DIFFRACTION19chain 'B' and (resid 145 through 180 )
20X-RAY DIFFRACTION20chain 'B' and (resid 181 through 205 )
21X-RAY DIFFRACTION21chain 'B' and (resid 206 through 242 )
22X-RAY DIFFRACTION22chain 'B' and (resid 243 through 275 )
23X-RAY DIFFRACTION23chain 'B' and (resid 276 through 297 )
24X-RAY DIFFRACTION24chain 'B' and (resid 298 through 356 )
25X-RAY DIFFRACTION25chain 'B' and (resid 357 through 396 )

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