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- PDB-6fi8: Crystal structure of the IS608 transposase in complex with left e... -

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Basic information

Entry
Database: PDB / ID: 6fi8
TitleCrystal structure of the IS608 transposase in complex with left end 29-mer DNA hairpin and a 6-mer DNA representing the intact target site: pre-cleavage target capture complex
Components
  • DNA 29-MER (LE29)
  • DNA 6-MER (T6')
  • Putative transposase
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / HUH MOTIF / DNA STEM LOOP / Transposition / TnpA transposase / target capture complex / ISHp608
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding / metal ion binding
Similarity search - Function
Transposase IS200 like / Transposase IS200-like / Transposase IS200-like / Transposase IS200-like superfamily / Transposase IS200 like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.598 Å
AuthorsMorero, N.R. / Barabas, O.
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Targeting IS608 transposon integration to highly specific sequences by structure-based transposon engineering.
Authors: Morero, N.R. / Zuliani, C. / Kumar, B. / Bebel, A. / Okamoto, S. / Guynet, C. / Hickman, A.B. / Chandler, M. / Dyda, F. / Barabas, O.
History
DepositionJan 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 28, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative transposase
B: Putative transposase
C: DNA 29-MER (LE29)
D: DNA 29-MER (LE29)
E: DNA 6-MER (T6')
F: DNA 6-MER (T6')
G: Putative transposase
H: Putative transposase
I: DNA 29-MER (LE29)
J: DNA 29-MER (LE29)
K: DNA 6-MER (T6')
L: DNA 6-MER (T6')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,01928
Polymers116,37812
Non-polymers64116
Water6,702372
1
A: Putative transposase
B: Putative transposase
C: DNA 29-MER (LE29)
D: DNA 29-MER (LE29)
E: DNA 6-MER (T6')
F: DNA 6-MER (T6')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,46913
Polymers58,1896
Non-polymers2817
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Putative transposase
H: Putative transposase
I: DNA 29-MER (LE29)
J: DNA 29-MER (LE29)
K: DNA 6-MER (T6')
L: DNA 6-MER (T6')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55015
Polymers58,1896
Non-polymers3619
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.640, 138.640, 117.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Putative transposase / Transposase / Transposase OrfA


Mass: 18392.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria)
Gene: BB387_02765, BB390_06935, BB392_05440, BB394_07800, BB413_07925, BB437_07715, BB438_04880, BB447_07970, BB453_04885, BB461_01775, BB469_00740, BFR58_04045, BFR58_04080, BFR58_04135, BFR58_ ...Gene: BB387_02765, BB390_06935, BB392_05440, BB394_07800, BB413_07925, BB437_07715, BB438_04880, BB447_07970, BB453_04885, BB461_01775, BB469_00740, BFR58_04045, BFR58_04080, BFR58_04135, BFR58_07690, BFR58_08055, BGL67_05025, BGL76_01750, BGL76_01790, BGL76_01830, BGL76_03945, BGL76_04370, BGL76_05875, BGL76_06710, BGL85_00790
Production host: Escherichia coli (E. coli) / References: UniProt: Q933Z0
#2: DNA chain
DNA 29-MER (LE29)


Mass: 8933.771 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori (bacteria)
#3: DNA chain
DNA 6-MER (T6')


Mass: 1768.205 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Helicobacter pylori (bacteria)
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 14.6% PEG 3350, 0.19 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.598→89.84 Å / Num. obs: 35947 / % possible obs: 99.72 % / Redundancy: 9.8 % / Biso Wilson estimate: 38.49 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.09723 / Rrim(I) all: 0.3091 / Net I/σ(I): 6.03
Reflection shellResolution: 2.598→2.691 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3525 / CC1/2: 0.738 / Rpim(I) all: 0.4295 / % possible all: 99.58

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VJV

2vjv


Resolution: 2.598→89.837 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.63
RfactorNum. reflection% reflection
Rfree0.2383 1795 5 %
Rwork0.1969 --
obs0.199 35890 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.598→89.837 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4145 2840 16 372 7373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037451
X-RAY DIFFRACTIONf_angle_d0.56210657
X-RAY DIFFRACTIONf_dihedral_angle_d20.6883974
X-RAY DIFFRACTIONf_chiral_restr0.0381204
X-RAY DIFFRACTIONf_plane_restr0.003852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5984-2.66860.34411280.30352570X-RAY DIFFRACTION100
2.6686-2.74720.35981180.29432588X-RAY DIFFRACTION100
2.7472-2.83580.32231430.28172585X-RAY DIFFRACTION100
2.8358-2.93720.29541280.26162597X-RAY DIFFRACTION100
2.9372-3.05480.29351360.2352577X-RAY DIFFRACTION100
3.0548-3.19380.25421390.2212614X-RAY DIFFRACTION100
3.1938-3.36220.22491490.19772580X-RAY DIFFRACTION100
3.3622-3.57290.23371450.18832614X-RAY DIFFRACTION100
3.5729-3.84880.18911530.17572588X-RAY DIFFRACTION100
3.8488-4.23610.19821350.15672651X-RAY DIFFRACTION100
4.2361-4.8490.17751260.14352644X-RAY DIFFRACTION100
4.849-6.1090.2471570.16462678X-RAY DIFFRACTION100
6.109-89.89050.24151380.20272809X-RAY DIFFRACTION99
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)
11.9126-0.7979-0.57461.0354-0.23921.3219-0.0395-0.1797-0.07960.0845-0.02380.06910.10380.01340.0110.2026-0.0043-0.01130.2055-0.00560.178-23.9238-1.621812.6274
22.283-0.3719-0.16560.34410.12410.82950.0178-0.002-0.1705-0.0216-0.02860.06520.0427-0.15180.02380.2066-0.0522-0.00180.2588-0.00180.2568-47.89691.155211.2799
31.7627-0.5480.03932.9211-0.83843.0380.1110.13750.2394-0.0794-0.0425-0.1161-0.3977-0.0583-0.11060.20640.04360.04540.22460.00010.2597-21.221411.3617-0.6312
41.47890.5239-0.041.9247-0.1093.4839-0.0406-0.29350.23780.19330.12270.1187-0.501-0.0593-0.08450.2420.02320.01720.3843-0.00570.3231-47.880813.125626.0488
51.8869-0.61692.5665.73020.85424.06550.05810.12870.1294-0.33330.00790.87870.2203-0.3243-0.23410.2120.06130.04980.2846-0.07790.3107-16.8298-4.5819-3.9884
65.50731.59692.27414.0051-1.99744.1820.06-0.5391-0.2370.4160.47160.14470.1138-0.6164-0.61730.2488-0.02430.02730.45430.09080.2556-56.0546-2.814227.0481
71.6123-0.29940.17181.89710.00971.8255-0.07180.00920.08470.0064-0.00490.0463-0.0104-0.05460.09450.2020.0015-0.01980.1950.02430.1949-71.379545.2029-17.6865
80.6654-0.2466-0.32552.53630.36120.8647-0.0642-0.0642-0.08110.15410.04010.0030.2161-0.03130.010.2963-0.021-0.01970.19580.00640.2249-67.935420.4014-16.7574
91.8658-0.62510.95420.83340.94963.71520.00020.14020.1288-0.02720.0514-0.22380.0460.4373-0.04540.28980.0122-0.01020.22120.01440.3182-57.580247.7131-5.3008
101.69610.6155-0.03452.47420.89463.86420.08370.1799-0.0647-0.13810.0933-0.2333-0.03970.4751-0.22630.3060.00110.01940.2413-0.01290.2953-57.265121.413-32.3596
113.6326-3.70941.22977.59860.24972.4796-0.53520.167-0.16880.32410.8689-0.4433-0.519-0.4951-0.20420.4154-0.05190.11990.3782-0.03340.2513-74.429352.5341-0.6573
125.5357-2.07322.05797.60752.06033.88740.1597-0.056-0.3453-0.16750.03230.33460.6789-0.1258-0.08030.3877-0.0073-0.07520.2280.03920.2138-72.435112.5522-32.1073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 132)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 133)
3X-RAY DIFFRACTION3(chain 'C' and resid 16 through 44)
4X-RAY DIFFRACTION4(chain 'D' and resid 16 through 44)
5X-RAY DIFFRACTION5(chain 'E' and resid -5 through 0)
6X-RAY DIFFRACTION6(chain 'F' and resid -5 through 0)
7X-RAY DIFFRACTION7(chain 'G' and resid 6 through 133)
8X-RAY DIFFRACTION8(chain 'H' and resid 6 through 130)
9X-RAY DIFFRACTION9(chain 'I' and resid 16 through 44)
10X-RAY DIFFRACTION10(chain 'J' and resid 16 through 44)
11X-RAY DIFFRACTION11(chain 'K' and resid -5 through 0)
12X-RAY DIFFRACTION12(chain 'L' and resid -5 through 0)

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