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- PDB-1u78: Structure of the bipartite DNA-binding domain of Tc3 transposase ... -

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Basic information

Entry
Database: PDB / ID: 1u78
TitleStructure of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA
Components
  • (26-MER) x 2
  • transposable element tc3 transposase
KeywordsDNA BINDING PROTEIN/DNA / transposase / transposon DNA / bipartite DNA-binding / HTH-motif / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


DNA integration / DNA recombination / DNA binding / nucleus
Similarity search - Function
Tc3 transposase, DNA binding domain / Tc1-like transposase, DDE domain / : / Tc3 transposase / DDE superfamily endonuclease / Transposable element Tc3 transposase, HTH / Homeodomain-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A ...Tc3 transposase, DNA binding domain / Tc1-like transposase, DDE domain / : / Tc3 transposase / DDE superfamily endonuclease / Transposable element Tc3 transposase, HTH / Homeodomain-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposable element Tc3 transposase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsWatkins, S. / van Pouderoyen, G. / Sixma, T.K.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Structural analysis of the bipartite DNA-binding domain of Tc3 transposase bound to transposon DNA
Authors: Watkins, S. / van Pouderoyen, G. / Sixma, T.K.
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Category: database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 26-MER
C: 26-MER
A: transposable element tc3 transposase


Theoretical massNumber of molelcules
Total (without water)32,1873
Polymers32,1873
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.681, 93.681, 255.558
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: DNA chain 26-MER


Mass: 7948.129 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 26-MER


Mass: 8028.177 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein transposable element tc3 transposase / Tc3 transposase


Mass: 16210.938 Da / Num. of mol.: 1 / Fragment: residues 1-135 / Mutation: E41V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: Tc3 / Plasmid: PET3C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P34257
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.93 Å3/Da / Density % sol: 77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Na acetate, glycerol, DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Na acetate11
2glycerol11
3DTT11
4Na acetate12
5glycerol12
6DTT12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0749 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0749 Å / Relative weight: 1
ReflectionResolution: 2.69→12 Å / Num. all: 18091 / Num. obs: 17820 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 101 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 20
Reflection shellResolution: 2.69→2.8 Å / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TC3

1tc3


Resolution: 2.69→12 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 10.488 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.275 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27291 954 5.1 %RANDOM
Rwork0.23329 ---
all0.23515 18091 --
obs0.23515 17820 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.441 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å2-0.97 Å20 Å2
2---1.94 Å20 Å2
3---2.91 Å2
Refinement stepCycle: LAST / Resolution: 2.69→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms816 1060 0 7 1883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212009
X-RAY DIFFRACTIONr_angle_refined_deg1.8972.6142925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9015102
X-RAY DIFFRACTIONr_chiral_restr0.0980.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021134
X-RAY DIFFRACTIONr_nbd_refined0.2170.2843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.23
X-RAY DIFFRACTIONr_mcbond_it0.5571.5514
X-RAY DIFFRACTIONr_mcangle_it1.0382829
X-RAY DIFFRACTIONr_scbond_it1.38831495
X-RAY DIFFRACTIONr_scangle_it2.0664.52096
LS refinement shellResolution: 2.689→2.755 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.479 67
Rwork0.456 1188

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