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- PDB-6cqi: 2.42A Crystal structure of Mycobacterium tuberculosis Topoisomera... -

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Basic information

Entry
Database: PDB / ID: 6cqi
Title2.42A Crystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with an oligonucleotide MTS2-11
Components
  • DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3')
  • DNA topoisomerase 1
KeywordsISOMERASE/DNA / Mycobacterium tuberculosis / Topoisomerase I / co-crystal / complex with oligonucleotide / Isomerase-DNA complex / ISOMERASE
Function / homology
Function and homology information


ribonuclease inhibitor activity / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / peptidoglycan-based cell wall / magnesium ion binding / DNA binding / plasma membrane / cytosol
Similarity search - Function
Topoisomerase C-terminal repeat / Topoisomerase C-terminal repeat / Topoisomerase I, domain 3 / 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 C-terminal repeat / Topoisomerase C-terminal repeat / Topoisomerase I, domain 3 / 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
ACETATE ION / FORMIC ACID / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsCao, N. / Thirunavukkarasu, A. / Tan, K. / Tse-Dinh, Y.-C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM054226 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
TB Alliance United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site.
Authors: Cao, N. / Tan, K. / Annamalai, T. / Joachimiak, A. / Tse-Dinh, Y.C.
History
DepositionMar 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA topoisomerase 1
B: DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5058
Polymers81,1442
Non-polymers3616
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-19 kcal/mol
Surface area32000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.777, 44.977, 129.229
Angle α, β, γ (deg.)90.00, 90.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain , 2 types, 2 molecules AB

#1: Protein DNA topoisomerase 1 / DNA topoisomerase I / Omega-protein / Relaxing enzyme / Swivelase / Untwisting enzyme


Mass: 77843.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: topA, Rv3646c, MTCY15C10.06 / Plasmid: PET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL / References: UniProt: P9WG49, EC: 5.99.1.2
#2: DNA chain DNA (5'-D(P*TP*TP*CP*CP*GP*CP*TP*TP*GP*A)-3')


Mass: 3300.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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Non-polymers , 4 types, 24 molecules

#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.46 Å3/Da / Density % sol: 50.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M ammonium phosphate dibasic, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 4, 2017 / Details: mirror
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.42→47 Å / Num. obs: 29799 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 55.9 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.047 / Χ2: 1.25 / Net I/σ(I): 19.5
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1268 / CC1/2: 0.818 / Rpim(I) all: 0.368 / Χ2: 0.642 / % possible all: 82.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UKT

5ukt
PDB Unreleased entry


Resolution: 2.42→47 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1484 5 %
Rwork0.2236 --
obs0.2259 29706 96.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5035 202 24 18 5279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045377
X-RAY DIFFRACTIONf_angle_d0.6567360
X-RAY DIFFRACTIONf_dihedral_angle_d13.5383183
X-RAY DIFFRACTIONf_chiral_restr0.042845
X-RAY DIFFRACTIONf_plane_restr0.004936
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4204-2.49850.31371110.32842207X-RAY DIFFRACTION83
2.4985-2.58780.3891160.31182418X-RAY DIFFRACTION93
2.5878-2.69140.36431430.30982558X-RAY DIFFRACTION98
2.6914-2.81380.3751140.30572608X-RAY DIFFRACTION98
2.8138-2.96220.3141400.27812605X-RAY DIFFRACTION99
2.9622-3.14770.37451170.27782644X-RAY DIFFRACTION99
3.1477-3.39070.36511410.2612601X-RAY DIFFRACTION99
3.3907-3.73180.2961410.23012609X-RAY DIFFRACTION98
3.7318-4.27150.22551560.19162618X-RAY DIFFRACTION100
4.2715-5.38040.22381610.18932637X-RAY DIFFRACTION99
5.3804-46.85420.23361440.19432717X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0229-0.46660.30631.741-0.87434.7943-0.1017-0.2428-0.13630.18810.29890.2476-0.0059-0.7805-0.16770.43890.02160.02390.46790.02050.350822.54211.253754.8104
22.13150.8811-1.44531.5859-0.99355.7737-0.28350.4765-0.3483-0.60660.2040.15411.1629-1.78220.12490.8906-0.2602-0.03740.9649-0.00050.51119.3819-6.703520.6018
31.3379-0.33430.6323.2116-3.5247.74690.11820.23540.165-0.2481-0.209-0.3787-0.47150.82920.08470.7332-0.08310.14420.5119-0.14280.513736.540311.676528.3251
47.11023.58230.08935.9503-0.85314.2811.0713-0.57091.09821.2961-0.33351.1438-1.8433-1.7202-0.42460.8860.1530.25980.785-0.01850.489218.77769.113548.5601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 211 )
2X-RAY DIFFRACTION2chain 'A' and (resid 212 through 573 )
3X-RAY DIFFRACTION3chain 'A' and (resid 574 through 704 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 11 )

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