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- PDB-5n8o: Cryo EM structure of the conjugative relaxes TraI of the F/R1 pla... -

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Entry
Database: PDB / ID: 5n8o
TitleCryo EM structure of the conjugative relaxes TraI of the F/R1 plasmid system
DescriptorDNA helicase I/DNA Complex
KeywordsTRANSFERASE / Relaxase / Cryo EM / Helicase / translocase / Transferase
Specimen sourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
MethodElectron microscopy (3.9 A resolution / Single particle)
AuthorsIlangovan, A. / Zanetti, G. / Waksman, G.
CitationCell, 2017, 169, 708-721.e12

Cell, 2017, 169, 708-721.e12 StrPapers
Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation.
Aravindan Ilangovan / Christopher W M Kay / Sandro Roier / Hassane El Mkami / Enrico Salvadori / Ellen L Zechner / Giulia Zanetti / Gabriel Waksman

DateDeposition: Feb 23, 2017 / Release: May 3, 2017 / Last modification: May 17, 2017

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Assembly

Deposited unit
A: DNA helicase I
C: DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)198,6442
Polyers198,6442
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (A2)5120
ΔGint (kcal/M)-48
Surface area (A2)67320
MethodPISA

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Components

#1: Polypeptide(L)DNA helicase I


Mass: 191996.734 Da / Num. of mol.: 1
Source: (gene. exp.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
References: UniProt: Q6TDU5
#2: DNA chainDNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')


Mass: 6647.284 Da / Num. of mol.: 1
Source: (synth.) Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeAssembly id
1TraI-22mer complexCOMPLEX1
2TraI proteinCOMPLEX1
322-mer DNA/RNA hybridCOMPLEX1
Specimen supportGrid material: GOLD / Grid type: quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 / Details: blot time 4 sec force 1

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 47619 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
EM image scansSampling size: 5 microns

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
ComputingStructure refinement: PHENIX (1.11.1_2575: phenix.real_space_refine)
3D reconstructionResolution: 3.9 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 184451 / Details: Relion automatic procedure / Number of class averages: 1
Atomic model buildingDetails: Please see article for details of model building and refinement
Ref space: REAL
Refine LS restraints
Refine idTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811560
ELECTRON MICROSCOPYf_angle_d1.24215708
ELECTRON MICROSCOPYf_dihedral_angle_d11.0489621
ELECTRON MICROSCOPYf_chiral_restr0.0651790
ELECTRON MICROSCOPYf_plane_restr0.0072015

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