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- PDB-6xgx: ISCth4 transposase, strand transfer complex 1, STC1 -

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Basic information

Entry
Database: PDB / ID: 6xgx
TitleISCth4 transposase, strand transfer complex 1, STC1
Components
  • DNA (21-MER)
  • DNA (25-MER)
  • DNA (47-MER)
  • 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 / 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 / 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 (47-MER)
E: DNA (25-MER)
F: DNA (21-MER)


Theoretical massNumber of molelcules
Total (without water)123,5635
Polymers123,5635
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-83 kcal/mol
Surface area50470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.570, 114.570, 232.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
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
132CYSCYSGLUGLU(chain 'A' and resid 262 through 335)AA262 - 335265 - 338
242CYSCYSGLUGLU(chain 'B' and resid 262 through 335)BB262 - 335265 - 338
153GLUGLUARGARG(chain 'A' and resid 336 through 406)AA336 - 406339 - 409
263GLUGLUARGARG(chain 'B' and resid 336 through 406)BB336 - 406339 - 409

NCS ensembles :
ID
1
2
3

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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 (47-MER)


Mass: 14450.340 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 (25-MER)


Mass: 7727.018 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)
#4: DNA chain DNA (21-MER)


Mass: 6389.186 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: 3.57 Å3/Da / Density % sol: 70 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, ammonium sulfate, PEG4000, zinc chloride

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: May 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.5→29.2 Å / Num. obs: 22945 / % possible obs: 99.8 % / Redundancy: 21.55 % / Biso Wilson estimate: 123.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.169 / Net I/σ(I): 14.54
Reflection shellResolution: 3.5→3.59 Å / Redundancy: 22.08 % / Rmerge(I) obs: 1.856 / Mean I/σ(I) obs: 2.15 / Num. unique obs: 1681 / CC1/2: 0.72 / % possible all: 100

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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→29.2 Å / SU ML: 0.4957 / Cross valid method: THROUGHOUT / σ(F): 2.15 / Phase error: 35.9559
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 1531 6.67 %random
Rwork0.2605 21407 --
obs0.2631 22938 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 160.52 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 1896 0 0 8062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00268401
X-RAY DIFFRACTIONf_angle_d0.57211728
X-RAY DIFFRACTIONf_chiral_restr0.041304
X-RAY DIFFRACTIONf_plane_restr0.00371161
X-RAY DIFFRACTIONf_dihedral_angle_d24.77043333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.610.42091380.33931904X-RAY DIFFRACTION100
3.61-3.740.37471360.31511912X-RAY DIFFRACTION100
3.74-3.890.3411390.29611912X-RAY DIFFRACTION100
3.89-4.070.36431340.29051926X-RAY DIFFRACTION100
4.07-4.280.28561380.26521911X-RAY DIFFRACTION100
4.28-4.550.30771400.25691942X-RAY DIFFRACTION99.95
4.55-4.90.31261350.25491926X-RAY DIFFRACTION99.95
4.9-5.390.31981380.25811951X-RAY DIFFRACTION100
5.39-6.160.35461400.29421957X-RAY DIFFRACTION100
6.16-7.740.31531420.28231985X-RAY DIFFRACTION100
7.74-29.20.22671510.21832081X-RAY DIFFRACTION99.78

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