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- PDB-2vhg: Crystal Structure of the ISHp608 Transposase in Complex with Righ... -

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Basic information

Entry
Database: PDB / ID: 2vhg
TitleCrystal Structure of the ISHp608 Transposase in Complex with Right End 31-mer DNA
Components
  • RIGHT END 31-MER
  • TRANSPOSASE ORFA
KeywordsDNA BINDING PROTEIN / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION / PROTEIN-DNA COMLPEX / DNA-BINDING PROTEIN
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: 2.9 Å
AuthorsBarabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection.
Authors: Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
History
DepositionNov 21, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSPOSASE ORFA
B: TRANSPOSASE ORFA
C: RIGHT END 31-MER
D: RIGHT END 31-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9265
Polymers55,8714
Non-polymers551
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-31.9 kcal/mol
Surface area22350 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.466, 90.925, 93.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.996639, 0.045058, 0.06841), (0.050682, -0.316905, 0.947102), (0.064354, 0.947386, 0.313556)40.8839, 29.4671, -23.2991
2given(-0.996639, 0.045058, 0.06841), (0.050682, -0.316905, 0.947102), (0.064354, 0.947386, 0.313556)40.8839, 29.4671, -23.2991

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Components

#1: Protein TRANSPOSASE ORFA / TRANSPOSASE / IS608 TRANSPOSASE


Mass: 18392.430 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: PECAN2A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q933Z0
#2: DNA chain RIGHT END 31-MER


Mass: 9543.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
Sequence detailsTHE ADDITION OF THE FIRST 5 RESIDUES (GSAMA) TO THE DATABASE SEQUENCE ARE THE RESULT OF CLONING ARTIFACT

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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: 2.5 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 6.5 / Details: 15-20% PEG 3350 AND 0.1 M MES PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Details: ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE-CRYSTAL (SI220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→40 Å / Num. obs: 13127 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25
Reflection shellResolution: 2.9→3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A6O

2a6o


Resolution: 2.9→40 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3197 843 6.5 %RANDOM
Rwork0.2847 ---
obs0.2847 11788 90.3 %-
Solvent computationBsol: 10 Å2 / ksol: 0.221686 e/Å3
Displacement parametersBiso mean: 86.2 Å2
Baniso -1Baniso -2Baniso -3
1--26.228 Å20 Å20 Å2
2--17.764 Å20 Å2
3---8.465 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.62 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.57 Å
Refinement stepCycle: LAST / Resolution: 2.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 958 1 0 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0055
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.591.5
X-RAY DIFFRACTIONc_mcangle_it2.952
X-RAY DIFFRACTIONc_scbond_it13.012
X-RAY DIFFRACTIONc_scangle_it12.742.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.445 117 7.9 %
Rwork0.403 1359 -
obs--70 %

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