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- PDB-1tc3: TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS -

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Basic information

Entry
Database: PDB / ID: 1tc3
TitleTRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS
Components
  • DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*GP*TP*CP*CP*TP*AP*TP*AP*GP*A P*AP*CP*TP*T)-3')
  • DNA (5'-D(*AP*GP*TP*TP*CP*TP*AP*TP*AP*GP*GP*AP*CP*CP*CP*CP*C P*CP*CP*T)-3')
  • PROTEIN (TC3 TRANSPOSASE)
KeywordsDNA BINDING PROTEIN/DNA / TRANSPOSASE / DNA BINDING / HELIX-TURN-HELIX / TC1/MARINER FAMILY / COMPLEX (TRANSPOSASE-DNA) / 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 / 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 / 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 / MIRAS / Resolution: 2.45 Å
AuthorsVan Pouderoyen, G. / Ketting, R.F. / Perrakis, A. / Plasterk, R.H.A. / Sixma, T.K.
CitationJournal: EMBO J. / Year: 1997
Title: Crystal structure of the specific DNA-binding domain of Tc3 transposase of C.elegans in complex with transposon DNA.
Authors: van Pouderoyen, G. / Ketting, R.F. / Perrakis, A. / Plasterk, R.H. / Sixma, T.K.
History
DepositionJul 7, 1997Deposition site: BNL / Processing site: NDB
Revision 1.0Nov 21, 1997Provider: repository / Type: Initial release
Revision 1.1May 22, 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 ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*GP*TP*CP*CP*TP*AP*TP*AP*GP*A P*AP*CP*TP*T)-3')
B: DNA (5'-D(*AP*GP*TP*TP*CP*TP*AP*TP*AP*GP*GP*AP*CP*CP*CP*CP*C P*CP*CP*T)-3')
C: PROTEIN (TC3 TRANSPOSASE)


Theoretical massNumber of molelcules
Total (without water)18,3873
Polymers18,3873
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.180, 202.790, 62.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(*AP*GP*GP*GP*GP*GP*GP*GP*TP*CP*CP*TP*AP*TP*AP*GP*A P*AP*CP*TP*T)-3')


Mass: 6543.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*AP*GP*TP*TP*CP*TP*AP*TP*AP*GP*GP*AP*CP*CP*CP*CP*C P*CP*CP*T)-3')


Mass: 6029.904 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (TC3 TRANSPOSASE)


Mass: 5813.720 Da / Num. of mol.: 1 / Fragment: SPECIFIC DNA BINDING DOMAIN, RESIDUES 2 - 52 / Mutation: C-TERMINAL 6-HIS TAG
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: BERGERAC / Gene: TC3A / Organelle: NUCLEUS / Variant: TR679 / Plasmid: PRP1200 / Cellular location (production host): CYTOPLASM / Gene (production host): TC3A N1-65 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P34257
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN/DNA COMPLEX WAS CRYSTALLIZED FROM 15% MPD, 100 MM NACL, 20 MM CACL2, 10 MM DTT, 50 MM NA ACETATE PH 5.5, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1WATER11
2MPD11
3NACL11
4CACL211
5DTT11
6NA ACETATE11
7WATER12
8MPD12
9NACL12
10CACL212
11DTT12
12NA ACETATE12
Crystal
*PLUS
Density % sol: 55 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mM1reservoirNaCl
220 mM1reservoirCaCl2
313-15 %MPD1reservoir
410 mMdithiothreitol1reservoir
550 mMsodium acetate1reservoir
650 mM1dropNaCl
710 mM1dropCaCl2
86.5-7.5 %1drop
95 mMdithiothreitol1drop
1025 mMsodium acetate1drop
112.25 mg/mlprotein1drop
121

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: BW7A SYSTEM
RadiationMonochromator: BW7A SYSTEM / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 8089 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.8 % / Biso Wilson estimate: 58.5 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 19.4
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.504 / Mean I/σ(I) obs: 1.93 / Rsym value: 0.504 / % possible all: 67
Reflection
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 30 Å / % possible obs: 89.7 % / Num. measured all: 70943
Reflection shell
*PLUS
% possible obs: 67.1 % / Rmerge(I) obs: 0.438

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Processing

Software
NameVersionClassification
PHASESphasing
TNT5-Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.45→20 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
Details: X-PLOR AND REFMAC/ARP WERE USED IN EARLIER STAGES OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.318 372 5 %RANDOM
all0.234 8071 --
obs0.234 8071 89 %-
Solvent computationSolvent model: TRONRUD ET AL. / Bsol: 150 Å2 / ksol: 0.75 e/Å3
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms404 834 0 49 1287
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01313430.8
X-RAY DIFFRACTIONt_angle_deg2.20719021.3
X-RAY DIFFRACTIONt_dihedral_angle_d20.447380
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00572
X-RAY DIFFRACTIONt_gen_planes0.0171015
X-RAY DIFFRACTIONt_it5.90912871
X-RAY DIFFRACTIONt_nbd0.0712510
Software
*PLUS
Name: TNT / Version: 5-E / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.45 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeWeightDev ideal
X-RAY DIFFRACTIONt_bond_d0.8
X-RAY DIFFRACTIONt_angle_deg1.3
X-RAY DIFFRACTIONt_dihedral_angle_d020.437
X-RAY DIFFRACTIONt_planar_d20.005
X-RAY DIFFRACTIONt_plane_restr50.017

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