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- PDB-2a6o: Crystal Structure of the ISHp608 Transposase in Complex with Stem... -

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Basic information

Entry
Database: PDB / ID: 2a6o
TitleCrystal Structure of the ISHp608 Transposase in Complex with Stem-loop DNA
Components
  • 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3'
  • ISHp608 Transposase
KeywordsTRANSCRIPTION/DNA / RNA Recognition Motif / DNA Stem-loop / TRANSCRIPTION-DNA COMPLEX
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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRonning, D.R. / Guynet, C. / Ton-Hoang, B. / Perez, Z.N. / Ghirlando, R. / Chandler, M. / Dyda, F.
CitationJournal: Mol.Cell / Year: 2005
Title: Active site sharing and subterminal hairpin recognition in a new class of DNA transposases.
Authors: Ronning, D.R. / Guynet, C. / Ton-Hoang, B. / Perez, Z.N. / Ghirlando, R. / Chandler, M. / Dyda, F.
History
DepositionJul 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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
C: 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3'
D: 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3'
A: ISHp608 Transposase
B: ISHp608 Transposase


Theoretical massNumber of molelcules
Total (without water)49,6994
Polymers49,6994
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.333, 71.132, 76.746
Angle α, β, γ (deg.)90.00, 94.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: DNA chain 5'-D(*CP*CP*CP*CP*TP*AP*GP*CP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*GP*A)-3'


Mass: 6743.353 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein ISHp608 Transposase


Mass: 18106.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pDR32 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q933Z0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 3350, Sodium Tartrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 24, 2004 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14684 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A6M

2a6m


Resolution: 2.6→44.2 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 324112.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1439 10.2 %RANDOM
Rwork0.209 ---
obs0.209 14083 95.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.2368 Å2 / ksol: 0.371023 e/Å3
Displacement parametersBiso mean: 38.5 Å2
Baniso -1Baniso -2Baniso -3
1-13.5 Å20 Å24.81 Å2
2---4.64 Å20 Å2
3----8.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2498 894 0 123 3515
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it3.271.5
X-RAY DIFFRACTIONc_mcangle_it5.142
X-RAY DIFFRACTIONc_scbond_it1.782
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 237 11 %
Rwork0.287 1911 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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