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

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Basic information

Entry
Database: PDB / ID: 6emz
TitleStructure of the Tn1549 transposon Integrase (aa 82-397, R225K) 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 / 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 / Core-binding (CB) domain / Tyrosine recombinase domain profile. / Core-binding (CB) domain profile. / Phage integrase family / Integrase, catalytic domain / 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: 2.79 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)99,5954
Polymers99,5954
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15420 Å2
ΔGint-122 kcal/mol
Surface area37290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.590, 125.060, 77.980
Angle α, β, γ (deg.)90.000, 96.530, 90.000
Int Tables number4
Space group name H-MP1211

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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 (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 / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 62.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M NH4-fluoride, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.52→48.36 Å / Num. obs: 40207 / % possible obs: 99.8 % / Redundancy: 5.6 % / CC1/2: 0.998 / Rsym value: 0.096 / Net I/av σ(I): 13.29 / Net I/σ(I): 13.29
Reflection shellResolution: 2.52→2.67 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.27 / CC1/2: 0.552 / Rsym value: 0.941 / % possible all: 79.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EMY

6emy


Resolution: 2.79→48.357 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.54
RfactorNum. reflection% reflection
Rfree0.2555 1467 4.94 %
Rwork0.1965 --
obs0.1994 29672 96.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.63 Å2 / Biso mean: 67.3522 Å2 / Biso min: 21.89 Å2
Refinement stepCycle: final / Resolution: 2.79→48.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 1453 0 122 6414
Biso mean---43.97 -
Num. residues----703
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026565
X-RAY DIFFRACTIONf_angle_d0.3999205
X-RAY DIFFRACTIONf_chiral_restr0.0311037
X-RAY DIFFRACTIONf_plane_restr0.003946
X-RAY DIFFRACTIONf_dihedral_angle_d17.4793669
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.79-2.88970.3121300.25872618274890
2.8897-3.00540.35391250.27232639276491
3.0054-3.14220.33241400.26352737287794
3.1422-3.30780.26131290.2272822295197
3.3078-3.5150.30261480.21762872302098
3.515-3.78630.2441580.20662873303199
3.7863-4.16710.2421660.17682874304099
4.1671-4.76970.23111520.162329103062100
4.7697-6.00750.24181590.179329193078100
6.0075-48.36470.22421600.174429413101100
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)
14.6684.6468-4.07827.5141-5.07625.36790.05720.0715-0.2964-0.2712-0.2555-0.4383-0.01630.45960.20920.42370.04330.04360.3015-0.01150.31028.3457-22.0537-22.5433
26.4006-0.65211.89362.18230.07243.8005-0.13450.49950.3508-0.02550.0457-0.2592-0.35030.41070.08710.4326-0.08570.0150.23920.03790.34685.9884-11.0231-19.1378
31.2520.48790.96020.17150.27210.69560.0266-0.12651.10730.01360.06591.257-0.1723-0.1886-0.05630.63940.11170.2920.4929-0.03930.8614-25.1719-15.4383-12.9754
42.1972-0.3632-0.51113.43960.48322.1773-0.1973-0.0751-0.17760.6620.05090.62120.0938-0.10990.10780.4721-0.02760.15030.2878-0.02530.4666-22.2293-32.6279-8.8638
53.4113-0.5565-0.63777.67425.81786.0458-0.53140.06150.4038-0.37060.07470.57670.4303-0.04540.35930.6147-0.1279-0.23910.41190.01240.4923-17.4175-11.37656.0756
66.41990.763-1.82626.4769-4.35333.1560.93391.66250.7871-0.77160.63181.3949-1.605-0.7173-1.0950.91890.1898-0.09271.0839-0.15371.153-31.6389-30.7112-32.4403
73.5622-1.7733-3.11114.32070.00343.53980.13410.49480.1794-0.32820.04610.4206-0.3236-0.5929-0.2470.3003-0.0045-0.04840.3613-0.040.2918-11.3049-25.802-21.7799
85.87354.36084.29473.3463.27413.1570.2865-0.987-0.941-1.07080.0083-2.0979-1.613-1.2424-0.42371.5265-0.3258-0.18571.26070.05380.98233.7641-14.82730.9866
93.66652.7367-2.6872.7477-2.32292.20081.0395-0.77280.16581.1506-0.6259-0.81690.1745-0.087-0.43810.8599-0.1534-0.13510.5270.0570.60038.53766.18330.8038
103.56623.1898-0.41552.2826-0.195-0.00310.3322-0.2994-0.98650.3138-0.0378-0.9820.1478-0.2715-0.31060.84270.0016-0.15490.49990.13980.84147.87053.412727.6022
113.1142.4493-0.86861.9518-0.72730.2855-0.3285-3.50730.72151.80630.3425-1.1756-0.7405-0.6523-0.5241.25590.1048-0.21190.9983-0.32460.73122.7093-11.1564-5.8634
122.9027-1.6785-1.76923.15230.663.6353-0.19920.9612-0.8675-0.7768-0.15790.5358-0.4356-1.19110.17930.60270.0167-0.07640.6173-0.15860.4762-18.9391-29.9517-25.8909
133.9944-1.1932-0.86944.76691.28723.2112-0.08980.4139-1.2908-0.31670.017-1.14820.58220.7207-0.01860.7590.09850.18240.6034-0.10031.210521.4683-5.444310.3718
142.53421.22441.142.2256-0.22470.8152-0.23340.582-0.59760.35240.2204-0.66911.01630.7965-0.79191.18810.09840.40270.1563-0.15491.518911.5353-15.119313.4335
153.49661.63040.18294.2061-0.89953.3312-0.13490.1899-0.0236-0.52170.03370.62980.2916-0.29160.09210.4610.0671-0.01650.1760.00160.4453-8.7918.613721.7647
165.76053.5911-2.30244.5219-0.40713.8010.2766-0.17410.32170.1786-0.27650.9429-0.1824-0.0107-0.07410.41830.0755-0.01140.259-0.00980.4611-8.396217.787424.8358
170.26722.38410.0933.2472.11121.5928-0.21770.0340.0183-0.1192-0.17340.18860.34030.04880.33140.66020.0155-0.01350.3580.01160.3964-10.3408-7.955820.7909
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 127 )A81 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 179 )A128 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 205 )A180 - 205
4X-RAY DIFFRACTION4chain 'A' and (resid 206 through 356 )A206 - 356
5X-RAY DIFFRACTION5chain 'A' and (resid 357 through 396 )A357 - 396
6X-RAY DIFFRACTION6chain 'C' and (resid -15 through -11 )C-15 - -11
7X-RAY DIFFRACTION7chain 'C' and (resid -10 through -1 )C-10 - -1
8X-RAY DIFFRACTION8chain 'C' and (resid 0 through 4 )C0 - 4
9X-RAY DIFFRACTION9chain 'C' and (resid 5 through 20 )C5 - 20
10X-RAY DIFFRACTION10chain 'E' and (resid -14 through 0 )E-14 - 0
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 5 )E1 - 5
12X-RAY DIFFRACTION12chain 'E' and (resid 6 through 20 )E6 - 20
13X-RAY DIFFRACTION13chain 'B' and (resid 81 through 164 )B81 - 164
14X-RAY DIFFRACTION14chain 'B' and (resid 165 through 192 )B165 - 192
15X-RAY DIFFRACTION15chain 'B' and (resid 193 through 275 )B193 - 275
16X-RAY DIFFRACTION16chain 'B' and (resid 276 through 314 )B276 - 314
17X-RAY DIFFRACTION17chain 'B' and (resid 315 through 396 )B315 - 396

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