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- PDB-1ecl: AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE... -

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Basic information

Entry
Database: PDB / ID: 1ecl
TitleAMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).
ComponentsESCHERICHIA COLI TOPOISOMERASE I
KeywordsTOPOISOMERASE / BACTERIAL TYPE I / DNA CLEAVAGE / STRAND PASSAGE
Function / homology
Function and homology information


DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding / cytosol
Similarity search - Function
DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I, domain 3 ...DNA topoisomerase I, zinc ribbon-like, bacterial-type / : / Topoisomerase I zinc-ribbon-like / Topoisomerase I, zinc finger / DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I, domain 3 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / DNA topoisomerase, type IA / DNA topoisomerase, type IA, central region, subdomain 2 / DNA topoisomerase, type IA, active site / Topoisomerase (Topo) IA-type active site signature. / Topoisomerase (Topo) IA-type catalytic domain profile. / Topoisomerase I; domain 3 / DNA topoisomerase, type IA, domain 2 / DNA topoisomerase, type IA, DNA-binding domain / DNA topoisomerase, type IA, central / DNA topoisomerase, type IA, central region, subdomain 1 / DNA topoisomerase, type IA, central region, subdomain 3 / DNA topoisomerase, type IA, core domain / DNA topoisomerase / Bacterial DNA topoisomeraes I ATP-binding domain / Bacterial DNA topoisomerase I DNA-binding domain / TOPRIM / Toprim domain / Toprim domain profile. / TOPRIM domain / Distorted Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsLima, C.D. / Wang, J.C. / Mondragon, A.
Citation
Journal: Nature / Year: 1994
Title: Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I.
Authors: Lima, C.D. / Wang, J.C. / Mondragon, A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of a 67 kDa Fragment of Escherichia Coli DNA Topoisomerase I
Authors: Lima, C.D. / Wang, J.C. / Mondragon, A.
History
DepositionMay 5, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ESCHERICHIA COLI TOPOISOMERASE I


Theoretical massNumber of molelcules
Total (without water)67,3261
Polymers67,3261
Non-polymers00
Water9,656536
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.190, 77.970, 138.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTHE ASYMMETRIC UNIT CONTAINS A SINGLE MOLECULE.

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Components

#1: Protein ESCHERICHIA COLI TOPOISOMERASE I / ESCHERICHIA COLI OMEGA PROTEIN


Mass: 67326.305 Da / Num. of mol.: 1
Mutation: GLY SER INSERTION AT N-TERMINUS, INSERTION OF STOP CODON AT 598; ENGINEERED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TOPA / Plasmid: PGEX-2T / Gene (production host): TOPA / References: UniProt: P06612, DNA topoisomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMOLECULE: AMINO-TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I. STRAND PASSAGE DOMAIN OF ...MOLECULE: AMINO-TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I. STRAND PASSAGE DOMAIN OF BACTERIAL TYPE I TOPOISOMERASES.
Sequence detailsRESIDUE NUMBERING IS FOR THE MATURE PROTEIN.
Source detailsMOLECULE_NAME: AMINO-TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I. ARTIFICIAL STOP ...MOLECULE_NAME: AMINO-TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I. ARTIFICIAL STOP CODON INTRODUCED AT AMINO ACID NUMBER 598 BY PCR TO PRODUCE A 67KDA POLYPEPTIDE FRAGMENT. EXPRESSION SYSTEM GENE EXPRESSED AS A FUSION PROTEIN WITH GLUTATHIONE-S-TRANSFERASE AT ITS AMINO-TERMINUS AND ENDING WITH AN ARTIFICIAL STOP CODON INTRODUCED AT AMINO ACID POSITION 598

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.58 %
Description: INITIAL PHASING WAS OBTAINED BY MULTIPLE ISOMORPHOUS PHASING TECHNIQUES USING A XENTRONICS/SIEMENS DETECTOR MOUNTED ON A RIGAKU RU200 GENERATOR (.1MM FOCUSING CUP). THE X-RAY BEAM WAS ...Description: INITIAL PHASING WAS OBTAINED BY MULTIPLE ISOMORPHOUS PHASING TECHNIQUES USING A XENTRONICS/SIEMENS DETECTOR MOUNTED ON A RIGAKU RU200 GENERATOR (.1MM FOCUSING CUP). THE X-RAY BEAM WAS FOCUSED WITH FRANK'S MIRRORS ON THE CRYSTAL POSITION. THE CRYSTALS USED IN MIR PHASING WERE FROZEN AT 100K FOR DATA COLLECTION. MIR PHASES WERE OBTAINED TO 3.0 ANGSTROMS AND A MODEL WAS SUBSEQUENTLY FIT INTO A SOLVENT FLATTED ELECTRON DENSITY MAP. THIS MODEL WAS TRANSFERRED TO A 2.11 ANGSTROM DATA SET COLLECTED AT 1.08 ANGSTROM WAVELENGTH AT THE STANFORD SYNCHROTRON RADIATION LABORATORY ON AN IP MAR SCANNER. THE MODEL WAS REFINED TO 2.2 ANGSTROMS WITH THIS DATA SET AND REPORTED IN LIMA (1994). THE MODEL WAS SUBSEQUENTLY TRANSFERRED TO A 1.7 ANGSTROM DATA SET COLLECTED AT 0.9144 ANGSTROM WAVELENGTH AT THE CORNELL HIGH ENERGY SYNCHROTRON SOURCE. THE DATA WAS COLLECTED ON THE PRINCETON CCD DETECTOR.
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Lima, C.D., (1993) J.Mol.Biol., 232, 1213.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12-10 mg/mlprotein1drop
250 mM1dropKCl
320 mMTris-HCl1drop
41 mMdithiothreitol1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Type: CHESS / Wavelength: 0.9144 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 23, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9144 Å / Relative weight: 1
ReflectionHighest resolution: 1.7 Å / Num. obs: 56798 / % possible obs: 80 % / Observed criterion σ(I): 4 / Redundancy: 2.9 % / Rmerge(I) obs: 0.059
Reflection
*PLUS
Highest resolution: 1.604 Å / Lowest resolution: 46.127 Å / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.9→5 Å / σ(F): 2
Details: INITIAL PHASING WAS OBTAINED BY MULTIPLE ISOMORPHOUS PHASING TECHNIQUES USING A XENTRONICS/SIEMENS DETECTOR MOUNTED ON A RIGAKU RU200 GENERATOR (.1MM FOCUSING CUP). THE X-RAY BEAM WAS ...Details: INITIAL PHASING WAS OBTAINED BY MULTIPLE ISOMORPHOUS PHASING TECHNIQUES USING A XENTRONICS/SIEMENS DETECTOR MOUNTED ON A RIGAKU RU200 GENERATOR (.1MM FOCUSING CUP). THE X-RAY BEAM WAS FOCUSED WITH FRANK'S MIRRORS ON THE CRYSTAL POSITION. THE CRYSTALS USED IN MIR PHASING WERE FROZEN AT 100K FOR DATA COLLECTION. MIR PHASES WERE OBTAINED TO 3.0 ANGSTROMS AND A MODEL WAS SUBSEQUENTLY FIT INTO A SOLVENT FLATTED ELECTRON DENSITY MAP. THIS MODEL WAS TRANSFERRED TO A 2.11 ANGSTROM DATA SET COLLECTED AT 1.08 ANGSTROM WAVELENGTH AT THE STANFORD SYNCHROTRON RADIATION LABORATORY ON AN IP MAR SCANNER. THE MODEL WAS REFINED TO 2.2 ANGSTROMS WITH THIS DATA SET AND REPORTED IN LIMA (1994). THE MODEL WAS SUBSEQUENTLY TRANSFERRED TO A 1.7 ANGSTROM DATA SET COLLECTED AT 0.9144 ANGSTROM WAVELENGTH AT THE CORNELL HIGH ENERGY SYNCHROTRON SOURCE. THE DATA WAS COLLECTED ON THE PRINCETON CCD DETECTOR. THE MODEL WAS REFINED TO 1.9 ANGSTROM WITH THIS DATA. THE COORDINATES THAT FOLLOW REPRESENT THIS REFINEMENT. A TOTAL OF 24 SIMULATED ANNEALING OMIT MAPS WERE GENERATED TO COVER THE ENTIRE STRUCTURE AT 1.9 ANGSTROM RESOLUTION. ALL THE RESIDUES INCLUDED IN THE MODEL WERE PRESENT IN THESE SIMULATED ANNEALING OMIT MAPS. RESIDUE ILE 34 IS THE ONLY OUTLIER WITH REGARDS TO A RAMACHANDRAN PLOT. IT WAS REMOVED DURING REFINEMENT AND ONLY REINSERTED AND REFINED AFTER DENSITY WAS OBSERVED FOR THE SIDE CHAIN ATOMS IN A SIMULATED ANNEALING OMIT MAP FOR THAT REGION.
RfactorNum. reflection% reflection
Rwork0.218 --
obs0.218 43060 83.4 %
Displacement parametersBiso mean: 30.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4404 0 0 536 4940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.868
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.47
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.896
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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