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- PDB-6en2: Structure of the Tn1549 transposon Integrase (aa 82-397, R225K) i... -

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Basic information

Entry
Database: PDB / ID: 6en2
TitleStructure of the Tn1549 transposon Integrase (aa 82-397, R225K) in complex with a circular intermediate DNA (CI6b-DNA)
Components
  • (DNA (45-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 / viral genome integration into host DNA / establishment of integrated proviral latency / DNA recombination / symbiont entry into host cell / 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
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Int protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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 (45-MER)
D: DNA (45-MER)
B: Int protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,5327
Polymers100,2134
Non-polymers3183
Water2,252125
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-111 kcal/mol
Surface area36210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.928, 132.725, 125.033
Angle α, β, γ (deg.)90.000, 90.100, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21B-503-

HOH

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Components

#1: Protein Int protein / Integrase


Mass: 36258.668 Da / Num. of mol.: 2 / Mutation: R225K
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 (45-MER)


Mass: 13838.937 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Enterococcus faecalis (bacteria)
#3: DNA chain DNA (45-MER)


Mass: 13856.968 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Circular intermediate DNA with 6 bp at the crossover region (CI6b: aaaggg)
Source: (synth.) Enterococcus faecalis (bacteria)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Crystal growTemperature: 293.15 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 6M / Detector: PIXEL / Date: Sep 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.48→68.471 Å / Num. obs: 42632 / % possible obs: 92.5 % / Redundancy: 2.6 % / CC1/2: 0.998 / Rrim(I) all: 0.074 / Rsym value: 0.06 / Net I/σ(I): 11.85
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 2.4 % / Num. unique obs: 2939 / CC1/2: 0.444 / Rrim(I) all: 1.156 / Rsym value: 0.929 / % possible all: 87

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Processing

Software
NameVersionClassification
BUSTERrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EN1

6en1


Resolution: 2.67→68.471 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 29.34
RfactorNum. reflection% reflection
Rfree0.2444 1631 4.77 %
Rwork0.1848 --
obs0.1877 34209 92.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 197.52 Å2 / Biso mean: 75.6002 Å2 / Biso min: 28.97 Å2
Refinement stepCycle: final / Resolution: 2.67→68.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 1466 51 125 6489
Biso mean--110.76 56.3 -
Num. residues----701
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)
14.04490.2342-1.10140.73760.03382.77720.115-0.10340.26590.2246-0.05960.1285-0.3040.0514-0.06950.4884-0.044-0.02360.35960.01760.5125-1.1936-117.406223.1869
28.58842.05262.84054.11122.16416.10780.04860.47860.4063-0.2919-0.1142-0.1538-0.42560.71570.07010.5036-0.05060.01180.57080.13020.389414.1964-114.77964.4273
31.4054-1.04380.59247.06894.18773.1418-0.3284-0.08160.01180.37380.58860.40560.15760.5846-0.27920.4986-0.01870.01570.56820.08360.528618.7037-113.491226.7709
43.98210.21181.3521-0.01380.61924.55230.1976-0.1412-0.3495-0.1918-0.21930.12450.2215-0.0735-0.0350.5978-0.04530.05510.39130.05110.51564.8247-126.469617.2931
55.83022.5820.26957.10651.67974.6910.0994-0.55781.0548-0.2429-0.1134-0.1351-1.02050.26190.02560.73090.01690.08520.6097-0.05650.69445.7436-68.820849.2001
64.7178-1.7905-1.82781.6149-0.68215.34750.5009-0.08410.4869-0.0806-0.61740.1104-0.4626-0.44620.07340.66090.00280.06510.47520.05390.57145.0929-73.265145.2105
76.7868-3.8923-1.27227.43051.93014.96350.04450.6627-1.01140.6314-0.3820.3151.05920.37090.31590.6828-0.0658-0.0420.6187-0.03630.51394.7166-128.749414.3954
85.70060.24810.8711.1312-0.10262.8229-0.00770.2596-0.0383-0.2002-0.01650.26310.2274-0.03310.00180.47880.0255-0.00210.2750.00780.4437-1.1839-81.942139.342
99.2352-7.0442-7.33147.63675.31469.0057-0.07440.1299-0.71390.0984-0.2720.4190.58730.19130.32810.44710.04630.00070.46540.03230.48459.6287-88.970254.1124
103.1368-0.2235-1.24452.00750.40873.92-0.0074-0.36130.050.0623-0.0112-0.1114-0.23110.75620.01240.2726-0.01710.00420.56690.00120.433517.9945-78.061750.5837
116.4231-0.8228-1.33254.40713.72627.3-0.94140.12250.6893-0.26080.76330.0537-0.51140.66170.11520.6884-0.136-0.09170.44880.02540.734319.2635-96.863830.0161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 242 )A81 - 242
2X-RAY DIFFRACTION2chain 'A' and (resid 243 through 314 )A243 - 314
3X-RAY DIFFRACTION3chain 'A' and (resid 315 through 395 )A315 - 395
4X-RAY DIFFRACTION4chain 'C' and (resid -16 through 5 )C-16 - 5
5X-RAY DIFFRACTION5chain 'C' and (resid 6 through 21 )C6 - 21
6X-RAY DIFFRACTION6chain 'D' and (resid -16 through 4 )D-16 - 4
7X-RAY DIFFRACTION7chain 'D' and (resid 5 through 21 )D5 - 21
8X-RAY DIFFRACTION8chain 'B' and (resid 81 through 242 )B81 - 242
9X-RAY DIFFRACTION9chain 'B' and (resid 243 through 275 )B243 - 275
10X-RAY DIFFRACTION10chain 'B' and (resid 276 through 356 )B276 - 356
11X-RAY DIFFRACTION11chain 'B' and (resid 357 through 395 )B357 - 395

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