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- PDB-3px7: Crystal Structure of covalent complex of topoisomerase 1A with su... -

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Basic information

Entry
Database: PDB / ID: 3px7
TitleCrystal Structure of covalent complex of topoisomerase 1A with substrate
Components
  • DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'
  • DNA 5'-D(*TP*TP*GP*GP*G)-3'
  • DNA topoisomerase
KeywordsISOMERASE/DNA / topoisomerase / ISOMERASE / ISOMERASE-DNA complex
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. / 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 / Topoisomerase I; domain 3 / 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
: / DNA / : / DNA topoisomerase 1
Similarity search - Component
Biological speciesEscherichia coli DH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhang, Z. / Tse-dinh, Y.C. / Cheng, B.
CitationJournal: To be Published
Title: Structure of E. coli Topoisomerase I Trapped as Covalent Complex Intermediate with Cleaved DNA
Authors: Tse-Dinh, Y.C. / Zhang, Z. / Cheng, B.
History
DepositionDec 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase
B: DNA 5'-D(*TP*TP*GP*GP*G)-3'
C: DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8576
Polymers71,2553
Non-polymers6023
Water2,522140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.602, 91.759, 141.976
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


Mass: 67277.125 Da / Num. of mol.: 1 / Fragment: residues 1-595 / Mutation: D111N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli DH1 (bacteria) / Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1 / Gene: 415337, EcDH1_2375 / Production host: Escherichia coli (E. coli)
References: UniProt: C9QXS7, UniProt: P06612*PLUS, DNA topoisomerase
#2: DNA chain DNA 5'-D(*TP*TP*GP*GP*G)-3'


Mass: 1551.046 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'


Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 288 K / pH: 6
Details: 0.2 M ammonium sulfate, 20% PEG4K, pH 6, VAPOR DIFFUSION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→500 Å / Num. obs: 65028 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rsym value: 0.09 / Net I/σ(I): 36.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRMethod rotation: fast direct / Method translation: &STRIP%trans_method

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→500 Å / Occupancy max: 1 / Occupancy min: 0.3 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.269 6470 9.4 %
Rwork0.23 --
obs0.23 65028 94.2 %
Solvent computationBsol: 52.96 Å2
Displacement parametersBiso mean: 50.25 Å2
Baniso -1Baniso -2Baniso -3
1--8.769 Å20 Å20 Å2
2--9.235 Å20 Å2
3----0.466 Å2
Refinement stepCycle: LAST / Resolution: 2.3→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4407 176 3 140 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4331.5
X-RAY DIFFRACTIONc_mcangle_it2.3722
X-RAY DIFFRACTIONc_scbond_it2.3822
X-RAY DIFFRACTIONc_scangle_it3.5322.5
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.371 107
Rwork0.2885 859
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP_MOD.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:DNA-RNA_REP.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4CNS_TOPPAR:ION.PARAM

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