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- PDB-1mw8: Crystal Structure of a Complex between H365R mutant of 67 kDA N-t... -

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Entry
Database: PDB / ID: 1mw8
TitleCrystal Structure of a Complex between H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I and 5'-ACTTCGGGATG-3'
Components
  • 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'
  • DNA Topoisomerase I
KeywordsISOMERASE / DNA TOPOISOMERASE / DECATENASE ENZYME / TOPRIM DOMAIN
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
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 / 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
THYMIDINE-5'-PHOSPHATE / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPerry, K. / Mondragon, A.
Citation
Journal: Structure / Year: 2003
Title: Structure of a Complex between E. coli DNA Topoisomerase I and Single-Stranded DNA.
Authors: Perry, K. / Mondragon, A.
#1: 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.
History
DepositionSep 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Oct 27, 2021Group: 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 1.6Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.7Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE THE AUTHOR'S SEQUENCE HAS ASN AT POSITION 549, WHICH HAS BEEN CONFIRMED BY SEQUENCING THE GENE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Y: 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'
X: DNA Topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1238
Polymers70,3202
Non-polymers8036
Water9,962553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.392, 79.148, 141.798
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: DNA chain 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'


Mass: 3389.221 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein DNA Topoisomerase I / Omega-protein / Relaxing enzyme / Untwisting enzyme / Swivelase


Mass: 66930.812 Da / Num. of mol.: 1 / Fragment: 67 kDa N-terminal fragment / Mutation: H365R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: TopA / Plasmid: pGEX-4T / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P06612, EC: 5.99.1.2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TMP / THYMIDINE-5'-PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.26 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulfate, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2(SO4)11
2(Na)(C2H3O2)11
3(Na)(C2H3O2)12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.1 Mammonium sulfate1reservoir
21
31

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11031
21031
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B10.95
SYNCHROTRONAPS 5ID-B20.95
Detector
TypeIDDetectorDate
MARRESEARCH1CCDDec 7, 2001
MARRESEARCH2CCDFeb 16, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→35 Å / Num. obs: 53723 / % possible obs: 95.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Rsym value: 0.061 / Net I/σ(I): 7.7
Reflection
*PLUS
Num. measured all: 209779
Reflection shell
*PLUS
% possible obs: 66.4 % / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALAdata scaling
CNSrefinement
MAR345data collection
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: H365R mutant, apo form

Resolution: 1.9→70.71 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27257 2846 5.1 %RANDOM
Rwork0.22346 ---
obs0.22595 52986 97.89 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.266 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--1.16 Å20 Å2
3----0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.9→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 126 46 553 5346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214895
X-RAY DIFFRACTIONr_bond_other_d0.0010.024346
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9926676
X-RAY DIFFRACTIONr_angle_other_deg0.726310127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7513594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg17.63715879
X-RAY DIFFRACTIONr_chiral_restr0.0790.2714
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02970
X-RAY DIFFRACTIONr_nbd_refined0.2790.31384
X-RAY DIFFRACTIONr_nbd_other0.240.34558
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.5533
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.3050.515
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.322
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.340
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2750.528
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7511.52897
X-RAY DIFFRACTIONr_mcangle_it1.41124701
X-RAY DIFFRACTIONr_scbond_it1.95631998
X-RAY DIFFRACTIONr_scangle_it3.3294.51975
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.317 176
Rwork0.28 3253
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 70 Å / Num. reflection Rfree: 2749 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65

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