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- PDB-1mw9: Crystal Structure of H365R mutant of 67 kDA N-terminal fragment o... -

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Basic information

Entry
Database: PDB / ID: 1mw9
TitleCrystal Structure of H365R mutant of 67 kDA N-terminal fragment of E. coli DNA Topoisomerase I
ComponentsDNA 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
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
X: DNA Topoisomerase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,79510
Polymers66,9311
Non-polymers8659
Water10,395577
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.990, 78.705, 139.328
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 / 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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 287 K / Method: dialysis / pH: 8 / Details: ammonium sulfate, pH 8, DIALYSIS, temperature 287K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 2.1 M / Common name: ammonium sulfate

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. all: 80202 / Num. obs: 79717 / % possible obs: 98.4 % / Observed criterion σ(I): 10737.6 / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.055 / Net I/σ(I): 8.2
Reflection
*PLUS
Num. measured all: 398050 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 98.4 % / Rmerge(I) obs: 0.407

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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: PDB ENTRY 1ECL

1ecl


Resolution: 1.67→49.39 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.785 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21638 3997 5 %RANDOM
Rwork0.20845 ---
obs0.20885 75645 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.686 Å2
Baniso -1Baniso -2Baniso -3
1--1.32 Å20 Å20 Å2
2--1.28 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.67→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 45 577 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214795
X-RAY DIFFRACTIONr_bond_other_d0.0010.024291
X-RAY DIFFRACTIONr_angle_refined_deg1.051.9566627
X-RAY DIFFRACTIONr_angle_other_deg0.671310023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.9843654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.7615900
X-RAY DIFFRACTIONr_chiral_restr0.0660.2695
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02978
X-RAY DIFFRACTIONr_nbd_refined0.2120.31198
X-RAY DIFFRACTIONr_nbd_other0.2140.34410
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.5481
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1040.55
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2610.339
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.364
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.527
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5021.52936
X-RAY DIFFRACTIONr_mcangle_it0.98224875
X-RAY DIFFRACTIONr_scbond_it1.46631859
X-RAY DIFFRACTIONr_scangle_it2.5784.51752
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.67→1.713 Å / Rfactor Rfree error: 0.11 / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.265 311
Rwork0.254 5558
obs-5558
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection obs: 75619 / Num. reflection Rfree: 4024 / Rfactor Rfree: 0.227 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.005
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.17

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