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- PDB-6pcm: Crystal Structure of Mycobacterium smegmatis Topoisomerase I with... -

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Basic information

Entry
Database: PDB / ID: 6pcm
TitleCrystal Structure of Mycobacterium smegmatis Topoisomerase I with ssDNA bound to both N- and C-terminal domains
Components
  • DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')
  • DNA topoisomerase 1
KeywordsISOMERASE/DNA / Topoisomerase I / ss DNA binding / N-terminal domain / C-terminal Domain / ISOMERASE-DNA complex
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA binding / metal ion binding
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 / 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. / DNA topoisomerase, type IA, domain 2 ...Topoisomerase C-terminal repeat / Topoisomerase C-terminal repeat / DNA topoisomerase I, bacterial-type / DNA topoisomerase I, type IA / DNA topoisomerase 1, TOPRIM domain / 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. / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
Mycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.107 Å
AuthorsTan, K. / Cao, N. / Tse-Dinh, Y.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM054226 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.
Authors: Cao, N. / Tan, K. / Zuo, X. / Annamalai, T. / Tse-Dinh, Y.C.
History
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: 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 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 topoisomerase 1
C: DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')
D: DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,62426
Polymers200,5114
Non-polymers2,11322
Water00
1
A: DNA topoisomerase 1
C: DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,40814
Polymers100,2552
Non-polymers1,15312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-145 kcal/mol
Surface area44050 Å2
MethodPISA
2
B: DNA topoisomerase 1
D: DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,21612
Polymers100,2552
Non-polymers96110
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-109 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.325, 135.067, 145.087
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 1 / DNA topoisomerase I


Mass: 92589.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: topA, MSMEG_6157, MSMEI_5999 / Plasmid: pET-His6-Mocr TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3)
References: UniProt: A0R5D9, DNA topoisomerase (ATP-hydrolysing)
#2: DNA chain DNA (5'-D(P*AP*GP*TP*GP*AP*GP*CP*GP*AP*GP*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*CP*TP*T)-3')


Mass: 7665.932 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycolicibacterium smegmatis (bacteria)
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
Has ligand of interestN

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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: 3.26 Å3/Da / Density % sol: 62.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris:HCl, 1.5M lithium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→47.5 Å / Num. obs: 47334 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 110 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.037 / Rrim(I) all: 0.083 / Χ2: 1.928 / Net I/σ(I): 29.9
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2351 / CC1/2: 0.764 / Rpim(I) all: 0.391 / Rrim(I) all: 0.938 / Χ2: 0.742 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQI

6cqi


Resolution: 3.107→47.442 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 2282 4.83 %random
Rwork0.2254 ---
obs0.2279 47242 98.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.107→47.442 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11351 984 110 0 12445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212752
X-RAY DIFFRACTIONf_angle_d0.44317629
X-RAY DIFFRACTIONf_dihedral_angle_d17.6517397
X-RAY DIFFRACTIONf_chiral_restr0.0372033
X-RAY DIFFRACTIONf_plane_restr0.0042152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1068-3.17440.40091410.36482715X-RAY DIFFRACTION97
3.1744-3.24820.37521360.34092793X-RAY DIFFRACTION100
3.2482-3.32940.32941470.32282803X-RAY DIFFRACTION100
3.3294-3.41940.35311540.2952758X-RAY DIFFRACTION99
3.4194-3.520.36411050.27892853X-RAY DIFFRACTION99
3.52-3.63350.28351240.24542753X-RAY DIFFRACTION98
3.6335-3.76340.29211380.24372804X-RAY DIFFRACTION100
3.7634-3.9140.32381530.24392816X-RAY DIFFRACTION100
3.914-4.0920.29141600.23652796X-RAY DIFFRACTION100
4.092-4.30760.30671510.21432818X-RAY DIFFRACTION99
4.3076-4.57730.24811320.20642791X-RAY DIFFRACTION98
4.5773-4.93040.26821430.19522761X-RAY DIFFRACTION97
4.9304-5.42590.24981580.21162845X-RAY DIFFRACTION99
5.4259-6.20960.30681310.23412859X-RAY DIFFRACTION99
6.2096-7.81770.28671420.22992844X-RAY DIFFRACTION98
7.8177-47.4480.22761670.19312951X-RAY DIFFRACTION97
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)
13.5199-2.2246-1.24952.67922.28512.1376-0.24090.21790.2104-0.60460.3443-0.43510.4213-0.1573-0.10711.1191-0.1661-0.01390.87650.03280.6033-21.0644-65.4645-29.2943
22.3943-1.1353-2.90162.11241.45143.5393-0.29890.0958-0.14840.33190.08340.36891.0315-0.82130.26861.8604-0.35050.02261.3209-0.0230.6607-37.4817-89.0133-5.4249
33.4371-0.1856-3.44740.01560.04753.875-0.4016-1.8002-0.16930.7858-0.42160.64381.19170.54910.79553.1648-0.48270.71261.66380.0351.5648-51.3385-99.19245.4221
41.7675-0.5401-0.36753.8412-0.66454.2611-0.02180.41410.0665-0.19090.07230.1009-0.0498-1.1142-0.0440.7889-0.1625-0.10511.1986-0.09160.6405-43.5953-57.3315-12.3293
55.08123.32191.87188.56932.84283.95750.5760.01840.42110.4805-0.1711-0.09020.1592-0.3088-0.27521.371-0.00250.03071.10090.11190.5652-44.3718-30.548731.1789
67.7894-1.5469-5.10284.5623-0.91688.2952-0.16680.86210.0145-1.0458-0.23740.7203-0.5028-0.70970.19451.2203-0.011-0.25081.0748-0.0330.6619-27.0477-1.853426.7844
70.9230.32611.22130.34440.46122.40720.03940.1267-0.13740.1792-0.01170.00830.07250.2585-0.02721.3874-0.20210.06510.87990.04430.67690.2007-17.939941.971
85.7784-1.41242.45380.735-0.21123.9079-0.2254-0.6152-0.22910.11580.23340.00880.4676-0.97870.05151.3236-0.17110.07130.86250.0250.6138-9.3778-17.39257.0443
91.2370.39790.9426-0.19130.33015.2356-0.0390.28050.29590.38560.1382-0.3454-0.82390.4917-0.07411.3084-0.35160.06080.93040.02310.75561.339-15.920533.6395
102.45460.4521-0.97.548-0.69330.2038-0.04791.0763-0.2212-1.03070.1036-1.0209-0.13120.8376-0.61131.1651-0.05040.05341.2859-0.29990.88688.6572-33.946713.0974
111.82022.54631.4125.52254.10434.40180.3316-0.0122-0.12430.22020.1034-0.99440.81170.9313-0.54771.36540.1851-0.31821.01450.00261.01162.7202-66.436-3.4094
125.32324.63535.23563.89674.79237.8975-0.56850.43580.3864-0.54370.7422-0.4276-0.81011.2952-0.2921.3367-0.1614-0.03191.3566-0.16070.8592-21.0306-34.979-8.1655
136.70125.03565.80128.3034.31024.56480.48710.1372-0.76860.9161-0.0849-2.09870.06171.354-0.21581.14210.0482-0.27061.614-0.08811.096-9.8707-64.2902-16.253
146.36365.62525.49655.02394.85854.6997-1.1650.8114-0.263-1.3120.6227-0.6695-1.3369-0.17950.55151.8542-0.0389-0.17191.4207-0.29831.4459-22.5716-31.2496-6.8478
158.59965.38946.48153.61874.22134.98591.76280.4854-1.77860.8402-0.51610.11841.2525-1.9963-2.13181.1875-0.1176-0.10511.1307-0.35171.0571-13.6583-14.623715.8465
163.6385-0.24690.50963.4521-3.70633.9491-2.97891.7713-3.7167-3.80060.504-0.43090.2827-0.61342.18361.5469-0.27970.08991.1204-0.16060.8749-22.7152-11.320332.9933
175.07336.2815.75127.71647.08716.5007-1.4628-1.3177-0.1329-3.15590.75032.6065-2.3025-0.83680.61571.653-0.1081-0.23151.49740.2661.139-40.45-21.81925.6343
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 208 )
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 439 )
3X-RAY DIFFRACTION3chain 'A' and (resid 440 through 498 )
4X-RAY DIFFRACTION4chain 'A' and (resid 499 through 691 )
5X-RAY DIFFRACTION5chain 'A' and (resid 692 through 838 )
6X-RAY DIFFRACTION6chain 'B' and (resid 13 through 99 )
7X-RAY DIFFRACTION7chain 'B' and (resid 100 through 320 )
8X-RAY DIFFRACTION8chain 'B' and (resid 321 through 464 )
9X-RAY DIFFRACTION9chain 'B' and (resid 465 through 618 )
10X-RAY DIFFRACTION10chain 'B' and (resid 619 through 710 )
11X-RAY DIFFRACTION11chain 'B' and (resid 711 through 839 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 16 )
13X-RAY DIFFRACTION13chain 'C' and (resid 17 through 25 )
14X-RAY DIFFRACTION14chain 'D' and (resid 2 through 11 )
15X-RAY DIFFRACTION15chain 'D' and (resid 12 through 16 )
16X-RAY DIFFRACTION16chain 'D' and (resid 17 through 21 )
17X-RAY DIFFRACTION17chain 'D' and (resid 22 through 25 )

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