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- PDB-6xgw: ISCth4 transposase, pre-reaction complex, PRC -

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Basic information

Entry
Database: PDB / ID: 6xgw
TitleISCth4 transposase, pre-reaction complex, PRC
Components
  • (DNA (32-MER)) x 2
  • Mutator family transposase
KeywordsRECOMBINATION / antibiotic resistance / promoter / transposon
Function / homologyTransposase, mutator type / Transposase, Mutator family / Transposases, Mutator family, signature. / transposase activity / DNA transposition / DNA binding / DNA / DNA (> 10) / Mutator family transposase
Function and homology information
Biological speciesHungateiclostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKosek, D. / Dyda, F.
CitationJournal: Embo J. / Year: 2021
Title: Structures of ISCth4 transpososomes reveal the role of asymmetry in copy-out/paste-in DNA transposition.
Authors: Kosek, D. / Hickman, A.B. / Ghirlando, R. / He, S. / Dyda, F.
History
DepositionJun 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.2Oct 18, 2023Group: 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: Mutator family transposase
B: Mutator family transposase
D: DNA (32-MER)
E: DNA (32-MER)


Theoretical massNumber of molelcules
Total (without water)114,6734
Polymers114,6734
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, analytical ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-76 kcal/mol
Surface area46350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.578, 99.050, 156.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Mutator family transposase / ISCth4 transposase


Mass: 47498.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0148, Cthe_0356, Cthe_0371, Cthe_1193, Cthe_1874, Cthe_3051
Production host: Escherichia coli (E. coli) / References: UniProt: A3DBR0
#2: DNA chain DNA (32-MER)


Mass: 9769.370 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
#3: DNA chain DNA (32-MER)


Mass: 9906.394 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)

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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: 3.02 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium cacodylate, calcium chloride, ammonium acetate, PEG4000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→46.07 Å / Num. obs: 17976 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 134.67 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.097 / Net I/σ(I): 10.94
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 3.87 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 1.78 / Num. unique obs: 1323 / CC1/2: 0.799 / % possible all: 99.66

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6XG8

6xg8


Resolution: 3.5→29.48 Å / SU ML: 0.5344 / Cross valid method: THROUGHOUT / σ(F): 1.78 / Phase error: 36.8918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 718 4 %random
Rwork0.2495 17232 --
obs0.2515 17950 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 154.77 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6159 1265 0 0 7424
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00277688
X-RAY DIFFRACTIONf_angle_d0.571310634
X-RAY DIFFRACTIONf_chiral_restr0.03991181
X-RAY DIFFRACTIONf_plane_restr0.00381129
X-RAY DIFFRACTIONf_dihedral_angle_d23.61823018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.770.39481410.3213399X-RAY DIFFRACTION99.35
3.77-4.150.35031410.30433367X-RAY DIFFRACTION99.07
4.15-4.750.3271430.28193432X-RAY DIFFRACTION99.28
4.75-5.970.32341440.27453459X-RAY DIFFRACTION99.61
5.97-29.480.2441490.20463575X-RAY DIFFRACTION98.99

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