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- PDB-6xg8: ISCth4 transposase, pre-cleaved complex, PCC -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6xg8
TitleISCth4 transposase, pre-cleaved complex, PCC
Components
  • (DNA (26-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 / MAD / 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 17, 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 1.2Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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 (26-MER)
E: DNA (26-MER)


Theoretical massNumber of molelcules
Total (without water)110,9674
Polymers110,9674
Non-polymers00
Water00
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-68 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.680, 109.500, 157.700
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROARGARG(chain 'A' and resid 164 through 261)AA164 - 261167 - 264
221PROPROARGARG(chain 'B' and resid 164 through 261)BB164 - 261167 - 264
132GLUGLUARGARG(chain 'A' and resid 336 through 406)AA336 - 406339 - 409
242GLUGLUARGARG(chain 'B' and resid 336 through 406)BB336 - 406339 - 409
153CYSCYSGLUGLU(chain 'A' and resid 262 through 335)AA262 - 335265 - 338
263CYSCYSGLUGLU(chain 'B' and resid 262 through 335)BB262 - 335265 - 338

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Mutator family transposase / ISCth4 transposase / protomer A


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 (26-MER)


Mass: 7914.155 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 (26-MER)


Mass: 8056.225 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: 3.49 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES, sodium chloride, sodium 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: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 22, 2017
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→29.61 Å / Num. obs: 20108 / % possible obs: 99.5 % / Redundancy: 7.17 % / Biso Wilson estimate: 148.31 Å2 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.078 / Net I/σ(I): 13.2
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 7.51 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1474 / CC1/2: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERrefinement
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.5→29.61 Å / SU ML: 0.5551 / Cross valid method: THROUGHOUT / σ(F): 1.8 / Phase error: 35.7569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 604 3 %
Rwork0.2208 19497 -
obs0.2222 20101 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 167.34 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6127 1060 0 0 7187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00357425
X-RAY DIFFRACTIONf_angle_d0.673210233
X-RAY DIFFRACTIONf_chiral_restr0.0441136
X-RAY DIFFRACTIONf_plane_restr0.00411113
X-RAY DIFFRACTIONf_dihedral_angle_d18.14344342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.850.37591480.29854792X-RAY DIFFRACTION99.8
3.85-4.410.33121490.27244810X-RAY DIFFRACTION99.62
4.41-5.550.32861510.25284864X-RAY DIFFRACTION99.96
5.55-29.610.21491560.18465031X-RAY DIFFRACTION99.33

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