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- PDB-2vih: CRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH Left E... -

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Basic information

Entry
Database: PDB / ID: 2vih
TitleCRYSTAL STRUCTURE OF THE IS608 TRANSPOSASE IN COMPLEX WITH Left END 26-MER DNA
Components
  • 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
  • TRANSPOSASE ORFA
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION
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: 2.1 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
DepositionDec 4, 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

Downloads & links

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Assembly

Deposited unit
A: TRANSPOSASE ORFA
B: TRANSPOSASE ORFA
C: 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'
D: 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3'


Theoretical massNumber of molelcules
Total (without water)52,7914
Polymers52,7914
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-32.3 kcal/mol
Surface area22170 Å2
MethodPQS
Unit cell
Length a, b, c (Å)73.482, 50.287, 115.554
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.963877, -0.253522, 0.081659), (-0.2606, 0.834304, -0.485823), (0.055038, -0.489554, -0.870234)115.843, 36.061, 74.344
2given(-0.959716, -0.270659, 0.075423), (-0.273716, 0.840006, -0.468477), (0.063441, -0.470249, -0.880251)116.762, 35.542, 73.135

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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 5'-D(*AP*AP*AP*GP*CP*CP*CP*CP*TP*AP *GP*CP*TP*TP*TP*TP*AP*GP*CP*TP*AP*TP*GP*GP*GP*G)-3' / LEFT END 26-MER


Mass: 8003.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
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: 1.93 Å3/Da / Density % sol: 41.5 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M SODIUM FORMATE AND 15-20% PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0332
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: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 24183 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 16.1
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.5 / % 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: 2.1→29.97 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 581756.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CHAIN A CONTAINS A FLEXIBLE LOOP REGION A133-A141, THAT FEATURES WEAK ELECTRON DENITIES AND HIGH B-FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 864 3.9 %RANDOM
Rwork0.225 ---
obs0.225 22051 92 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.7319 Å2 / ksol: 0.309741 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1-22.92 Å20 Å2-7.04 Å2
2---6.16 Å20 Å2
3----16.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 1041 0 86 3412
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.35
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.691.5
X-RAY DIFFRACTIONc_mcangle_it2.912
X-RAY DIFFRACTIONc_scbond_it11.572
X-RAY DIFFRACTIONc_scangle_it11.892.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 129 3.8 %
Rwork0.363 3232 -
obs--85.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLWATER.TOP

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