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- PDB-2a6m: Crystal Structure of the ISHp608 Transposase -

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Basic information

Entry
Database: PDB / ID: 2a6m
TitleCrystal Structure of the ISHp608 Transposase
ComponentsISHp608 transposase
KeywordsTRANSCRIPTION/DNA / RNA Recognition Motif / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA 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
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
A: ISHp608 transposase
B: ISHp608 transposase


Theoretical massNumber of molelcules
Total (without water)36,2122
Polymers36,2122
Non-polymers00
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-24 kcal/mol
Surface area14730 Å2
MethodPISA
2
A: ISHp608 transposase
B: ISHp608 transposase

A: ISHp608 transposase
B: ISHp608 transposase


Theoretical massNumber of molelcules
Total (without water)72,4254
Polymers72,4254
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11670 Å2
ΔGint-63 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.520, 50.976, 52.921
Angle α, β, γ (deg.)90.00, 105.45, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biologically relevant molecule is the dimer in the asymmetric unit.

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Components

#1: 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: pDR32B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q933Z0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, Sodium Thiocyanate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU RU20011.54178
SYNCHROTRONAPS 22-ID20.9796, 0.9794, 0.9687
Detector
TypeIDDetectorDateDetails
RIGAKU RAXIS IV1IMAGE PLATEJun 24, 2004mirrors
MARMOSAIC 300 mm CCD2CCDMar 15, 2004mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541781
20.97961
30.97941
40.96871
ReflectionResolution: 2.4→50 Å / Num. obs: 12555 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.043 / Net I/σ(I): 28.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→22.8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1105901.61 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 562 4.6 %RANDOM
Rwork0.254 ---
obs0.254 12250 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6966 Å2 / ksol: 0.297548 e/Å3
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1--12.2 Å20 Å25.55 Å2
2--20.53 Å20 Å2
3----8.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→22.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 0 63 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.561.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it3.092
X-RAY DIFFRACTIONc_scangle_it3.722.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.394 98 5 %
Rwork0.312 1871 -
obs--94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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