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- PDB-6en1: Structure of the Tn1549 transposon Integrase (aa 82-397, R225K) i... -

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Basic information

Entry
Database: PDB / ID: 6en1
TitleStructure of the Tn1549 transposon Integrase (aa 82-397, R225K) in complex with a circular intermediate DNA (CI6a-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 / 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
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 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 (45-MER)
D: DNA (45-MER)
B: Int protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4246
Polymers100,2114
Non-polymers2122
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-108 kcal/mol
Surface area37880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.740, 123.880, 77.750
Angle α, β, γ (deg.)90.000, 118.210, 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 (45-MER)


Mass: 13877.974 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: 13815.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Circular intermediate DNA with 6 bp at the crossover region (CI6a: gaaaat)
Source: (synth.) Enterococcus faecalis (bacteria)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
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 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→45.392 Å / Num. obs: 39879 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 55.71 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.156 / Rsym value: 0.133 / Net I/σ(I): 8.19
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 10875 / CC1/2: 0.492 / Rrim(I) all: 1.523 / Rsym value: 1.3 / % possible all: 97.2

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Processing

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

6emy


Resolution: 2.67→45.392 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.2436 1868 5.08 %
Rwork0.1881 --
obs0.191 36788 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.25 Å2 / Biso mean: 65.2466 Å2 / Biso min: 19.88 Å2
Refinement stepCycle: final / Resolution: 2.67→45.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4913 1545 34 131 6623
Biso mean--84.98 45.12 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046751
X-RAY DIFFRACTIONf_angle_d0.5949451
X-RAY DIFFRACTIONf_chiral_restr0.0351056
X-RAY DIFFRACTIONf_plane_restr0.004958
X-RAY DIFFRACTIONf_dihedral_angle_d17.5513780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.74220.33531460.286226602806100
2.7422-2.82290.32351370.263926542791100
2.8229-2.9140.34261470.278126922839100
2.914-3.01810.3661590.276326582817100
3.0181-3.13890.36211360.275727192855100
3.1389-3.28170.32091300.23526402770100
3.2817-3.45470.27971450.210126892834100
3.4547-3.6710.2461430.186826972840100
3.671-3.95430.23541430.167926952838100
3.9543-4.3520.21631380.151826892827100
4.352-4.98110.2071490.139927012850100
4.9811-6.2730.19211400.164226992839100
6.273-45.39860.18911550.16442727288299
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)
12.3418-0.73560.81632.3727-0.84793.21690.0061-0.2102-0.1983-0.1337-0.1328-0.21120.23140.15190.00010.39170.00490.04980.43140.07530.3546-82.7189-15.969388.9108
21.70190.061-0.28571.3661-0.31291.56750.08530.4119-0.1207-0.3318-0.00540.49760.2873-0.1048-0.00020.5104-0.0929-0.0950.4193-0.02760.5047-106.8687-9.362563.0215
3-0.1514-0.53180.08982.46550.7312.9340.05370.00110.0656-0.3003-0.04620.0436-0.15690.1575-00.3364-0.0094-0.02580.3469-0.0110.3387-97.94774.672363.7563
40.1809-0.9487-1.18090.01542.13370.00630.31770.1133-0.5697-0.2195-0.27950.2928-0.057-0.2024-0.03060.45160.041-0.01860.4596-0.03790.4835-93.6109-18.168956.2747
5-0.00310.005-0.00490.0815-0.15690.25420.1117-1.19781.47250.4073-0.68790.0025-0.1826-0.4082-0.01851.5167-0.22490.50171.2146-0.48191.5867-125.9557-0.643182.4057
60.39790.67021.15711.66941.33272.0669-0.04170.25710.25750.24020.0069-0.18710.0385-0.07920.00070.441-0.00460.13310.49250.07150.4017-96.0258-6.032476.8376
71.24830.10171.15180.5022-0.68191.5907-0.1064-0.17530.4272-0.00770.04060.0605-0.4023-0.018500.4213-0.0320.0290.4915-0.020.4479-62.9774-29.181761.1445
82.4513-1.8151-2.0391.03091.25971.75620.6769-0.060.603-1.41980.1504-1.03690.95040.66290.63911.18730.22960.04710.80870.09610.9595-44.9637-41.720438.8029
90.2549-0.02540.2640.0037-0.02590.2951-0.6432-0.5930.6919-0.7889-0.3054-1.14840.17530.6847-0.02710.94880.15580.37771.15420.54462.1223-39.2061-38.98630.1829
100.841-0.78520.7431.6876-1.39591.03670.22150.17240.31420.1929-0.1465-0.28160.2802-0.173-0.00030.3809-0.01650.04780.4172-0.02240.497-58.5813-32.673455.3359
112.13040.41781.24712.91880.3641.0295-0.8249-0.05570.21190.42350.03310.76890.0468-0.2037-0.47240.4527-0.06080.05920.4601-0.11050.4955-107.0263-2.018279.0413
121.36420.16130.03712.52480.94123.06610.0463-0.20680.25780.0752-0.07370.0116-0.26230.116-00.3554-0.0441-0.01990.4242-0.05520.3981-54.3072-23.566771.9899
131.33530.15180.22120.95070.08531.5473-0.07790.17760.113-0.37730.01270.107-0.2338-0.29430.00030.5751-0.0089-0.06580.3640.05160.3864-65.6273-30.028738.4859
141.5826-1.1051.4660.7799-0.38110.9582-0.1315-0.38210.1213-0.023-0.0740.3276-0.0137-0.31240.00010.32720.0078-0.0230.4337-0.01290.4265-73.5754-43.437751.9228
152.0562-0.03490.80952.87120.43320.53030.17240.1925-0.1117-0.3216-0.01630.06040.12560.0215-0.00010.35160.0099-0.01230.3936-0.00220.3139-65.6161-44.864741.9526
160.521-3.0331-0.65170.39790.3774-0.56910.3701-0.0717-0.1842-0.3718-0.17130.101-0.54110.03810.05640.55520.03930.01780.4564-0.03010.4107-77.8388-21.184646.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 179 )A81 - 179
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 222 )A180 - 222
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 332 )A223 - 332
4X-RAY DIFFRACTION4chain 'A' and (resid 333 through 396 )A333 - 396
5X-RAY DIFFRACTION5chain 'C' and (resid -17 through -13 )C-17 - -13
6X-RAY DIFFRACTION6chain 'C' and (resid -12 through 2 )C-12 - 2
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 12 )C3 - 12
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 22 )C13 - 22
9X-RAY DIFFRACTION9chain 'D' and (resid -17 through -13 )D-17 - -13
10X-RAY DIFFRACTION10chain 'D' and (resid -12 through 5 )D-12 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 23 )D6 - 23
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 179 )B81 - 179
13X-RAY DIFFRACTION13chain 'B' and (resid 180 through 222 )B180 - 222
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 275 )B223 - 275
15X-RAY DIFFRACTION15chain 'B' and (resid 276 through 332 )B276 - 332
16X-RAY DIFFRACTION16chain 'B' and (resid 333 through 396 )B333 - 396

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