+Open data
-Basic information
Entry | Database: PDB / ID: 1tc3 | ||||||
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Title | TRANSPOSASE TC3A1-65 FROM CAENORHABDITIS ELEGANS | ||||||
Components |
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Keywords | DNA 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 | ||||||
Biological species | Caenorhabditis elegans (invertebrata) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.45 Å | ||||||
Authors | Van Pouderoyen, G. / Ketting, R.F. / Perrakis, A. / Plasterk, R.H.A. / Sixma, T.K. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tc3.cif.gz | 47.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tc3.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 1tc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tc3_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
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Full document | 1tc3_full_validation.pdf.gz | 452.2 KB | Display | |
Data in XML | 1tc3_validation.xml.gz | 8 KB | Display | |
Data in CIF | 1tc3_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/1tc3 ftp://data.pdbj.org/pub/pdb/validation_reports/tc/1tc3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6543.232 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 6029.904 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | 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 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: 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 |
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Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1996 / Details: BW7A SYSTEM |
Radiation | Monochromator: BW7A SYSTEM / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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 |
-Processing
Software |
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Refinement | Method 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.
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Solvent computation | Solvent model: TRONRUD ET AL. / Bsol: 150 Å2 / ksol: 0.75 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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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
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