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- PDB-1cy6: COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3' THYMIDINE MONOPHOSPHATE -

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Basic information

Entry
Database: PDB / ID: 1cy6
TitleCOMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3' THYMIDINE MONOPHOSPHATE
ComponentsDNA TOPOISOMERASE I
KeywordsISOMERASE / DNA TOPOISOMERASE / RELAXING ENZYME
Function / homology
Function and homology information


RNA topoisomerase activity / DNA topoisomerase activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / zinc ion binding / cytosol
Similarity search - Function
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 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 ...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 / Topoisomerase I; domain 2 / Topoisomerase I, domain 2 / Rossmann fold - #140 / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / Topoisomerase I; domain 4 / Topoisomerase I, domain 4 / Topoisomerase I; domain 3 / 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. / 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
PHOSPHATE ION / THYMIDINE-3'-PHOSPHATE / DNA topoisomerase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFeinberg, H. / Changela, A. / Mondragon, A.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Protein-nucleotide interactions in E. coli DNA topoisomerase I.
Authors: Feinberg, H. / Changela, A. / Mondragon, A.
History
DepositionAug 31, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TOPOISOMERASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1505
Polymers67,5431
Non-polymers6074
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.630, 80.720, 143.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA TOPOISOMERASE I


Mass: 67542.500 Da / Num. of mol.: 1
Fragment: 67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: PGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 ALPHA / References: UniProt: P06612, EC: 5.99.1.2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-T3P / THYMIDINE-3'-PHOSPHATE / ALPHA-ANOMERIC THYMIDINE-3'-PHOSPHATE


Type: DNA linking / Mass: 322.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.2M AMMONIUM SULFATE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: and 14 degrees centigrade
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.5-6 mg/mlprotein1drop
21.45-20 mMnucleotide1drop
32.2-2.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.008
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 2.5→999 Å / Num. all: 256045 / Num. obs: 26758 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.067
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.296 / % possible all: 80.9
Reflection
*PLUS
Num. measured all: 256045
Reflection shell
*PLUS
% possible obs: 80.9 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
REFMACrefinement
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.5→19.99 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1437987.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: R. A. ENGH AND R. HUBER, ACTA CRYST. SECT. A., 1991
Details: REFINEMENT DONE WITH REFMAC. THE SOLVENT CORRECTION WAS CALCULATED WITH XPLOR AND APPLIED IN REFMAC. FINAL PARAMETERS OBTAINED WITH CNS 0.9
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1065 4.6 %RANDOM
Rwork0.244 ---
all0.244 23321 --
obs0.244 23321 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å20 Å20 Å2
2--6.75 Å20 Å2
3----5.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-20 Å
Luzzati sigma a0.4 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 36 109 4627
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.84
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.021.5
X-RAY DIFFRACTIONx_mcangle_it1.82
X-RAY DIFFRACTIONx_scbond_it1.342
X-RAY DIFFRACTIONx_scangle_it2.122.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.396 147 4.1 %
Rwork0.358 3400 -
obs--81.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION23TP.PAR3TP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: 'X-PLOR,REFMAC,CNS 0.9' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.84

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