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- PDB-6cq2: Crystal structure of Mycobacterium tuberculosis Topoisomerase I i... -

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Basic information

Entry
Database: PDB / ID: 6cq2
TitleCrystal structure of Mycobacterium tuberculosis Topoisomerase I in complex with oligonucleotide MTS2-12 and Magnesium
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-crystallization / complex with oligonucleotide and Magnesium / ISOMERASE / ISOMERASE-DNA complex
Function / homology
Function and homology information


negative regulation of ribonuclease 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 / 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 C-terminal repeat / Topoisomerase C-terminal repeat / 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. / Topoisomerase I; domain 3 / 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 / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.004 Å
AuthorsCao, N. / Thirunavukkaraus, 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 14, 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 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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)81,9447
Polymers81,7522
Non-polymers1925
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-61 kcal/mol
Surface area32620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.625, 44.683, 128.866
Angle α, β, γ (deg.)90.00, 90.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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) / 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: 3908.545 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Mycobacterium tuberculosis H37Rv (bacteria)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Acetate, 0.1 M MES NaOH, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2016
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→37.5 Å / Num. obs: 15372 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.091 / Rrim(I) all: 0.161 / Χ2: 1.21 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.816 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 967 / CC1/2: 0.5 / Rpim(I) all: 0.565 / Χ2: 0.839 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 3.004→37.279 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.45
RfactorNum. reflection% reflectionSelection details
Rfree0.249 735 4.79 %random
Rwork0.1885 ---
obs0.1916 15348 97.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.004→37.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5289 202 9 14 5514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025623
X-RAY DIFFRACTIONf_angle_d0.4187682
X-RAY DIFFRACTIONf_dihedral_angle_d14.1833369
X-RAY DIFFRACTIONf_chiral_restr0.037867
X-RAY DIFFRACTIONf_plane_restr0.004976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0038-3.23560.32941500.27142842X-RAY DIFFRACTION96
3.2356-3.5610.38771430.23912901X-RAY DIFFRACTION98
3.561-4.07570.26271240.19652971X-RAY DIFFRACTION99
4.0757-5.13290.23651590.16052915X-RAY DIFFRACTION98
5.1329-37.28230.19191590.16492984X-RAY DIFFRACTION96
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)
16.50823.3362-1.23364.9845-0.94363.32850.0694-0.69020.12150.43560.06220.4654-0.1509-0.4738-0.10.4410.1306-0.05610.49490.00930.22919.53534.145261.1706
21.6965-0.4707-0.73792.4947-1.60625.50940.0321-0.0884-0.1805-0.01730.0658-0.02310.1492-0.2087-0.07560.2446-0.0165-0.12380.2244-0.07150.277324.27171.778746.8423
30.92470.78240.21940.22990.57594.973-0.04630.2062-0.0475-0.40040.04730.06790.0927-0.31750.03440.73440.086-0.05070.2988-0.01210.37510.0982-6.209812.9104
47.56871.08280.27888.17571.82027.1467-0.0597-0.0215-0.2990.31890.01860.42360.9577-1.36280.04180.7081-0.1964-0.01240.68920.08940.3143-1.837-10.628937.7117
51.07370.71751.09871.62911.31693.12610.0087-0.0037-0.1977-0.3630.0998-0.05270.2057-0.1708-0.12620.63570.02980.03340.3665-0.04330.308917.1824-3.115121.5748
62.70970.85380.33736.5574-2.81732.2373-0.0920.1910.2886-1.6689-0.3265-1.39060.23131.13460.37470.7972-0.15350.24030.7629-0.12230.573444.00469.172236.0241
75.46860.07911.9596.75071.26594.73270.2054-0.1460.3864-0.18460.0551-0.2929-0.37180.0561-0.25141.0088-0.07660.10930.46240.03910.363731.597726.686514.2433
83.18563.5714-2.28174.0483-2.90874.79330.0841-0.77711.09021.39550.39580.8595-2.1576-1.2334-0.30650.46230.4448-0.0540.54920.13020.603318.139111.004348.1965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 16 through 127 )
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 351 )
4X-RAY DIFFRACTION4chain 'A' and (resid 352 through 431 )
5X-RAY DIFFRACTION5chain 'A' and (resid 432 through 608 )
6X-RAY DIFFRACTION6chain 'A' and (resid 609 through 643 )
7X-RAY DIFFRACTION7chain 'A' and (resid 644 through 704 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 10 )

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