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- PDB-8czq: The crystal structure of MtbTOP1 in complex with both G- and T-se... -

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Basic information

Entry
Database: PDB / ID: 8czq
TitleThe crystal structure of MtbTOP1 in complex with both G- and T-segments
Components
  • DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
  • DNA topoisomerase 1Topoisomerase
KeywordsISOMERASE/DNA / topoisomerase 1 / MYCOBACTERIUM TUBERCULOSIS / G-segment / T-segment / ISOMERASE / 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
ACETATE ION / PHOSPHATE ION / DNA / DNA (> 10) / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsTan, K. / Tse-Dinh, Y.-C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01GM054226 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139817 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: The interaction between transport-segment DNA and topoisomerase IA-crystal structure of MtbTOP1 in complex with both G- and T-segments.
Authors: Ferdous, S. / Dasgupta, T. / Annamalai, T. / Tan, K. / Tse-Dinh, Y.C.
History
DepositionMay 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: 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 1.2Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
C: DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
D: DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,70017
Polymers88,6124
Non-polymers1,08813
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-54 kcal/mol
Surface area37750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.501, 98.632, 104.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein DNA topoisomerase 1 / Topoisomerase / DNA topoisomerase I


Mass: 77843.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: topA_1, topA, BN1213_00605, BN1303_02614, ERS013471_01645, ERS027644_01463, ERS124361_02532, RN05_3882
Plasmid: ET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL / References: UniProt: A0A0E8VY41, DNA topoisomerase
#2: DNA chain DNA (5'-D(*CP*TP*TP*CP*CP*GP*CP*TP*TP*GP*AP*C)-3')


Mass: 3589.341 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
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: 2.68 Å3/Da / Density % sol: 54.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M sodium acetate, trihydrate, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2017 / Details: mirror
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→46.5 Å / Num. obs: 24480 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 82.81 Å2 / CC1/2: 0.982 / CC star: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/av σ(I): 1.138 / Net I/σ(I): 23.5
Reflection shellResolution: 2.78→2.83 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.372 / Num. unique obs: 1195 / CC1/2: 0.49 / CC star: 0.811 / R split: 1.15 / Rpim(I) all: 0.614 / Χ2: 0.642 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CQI

6cqi


Resolution: 2.78→46.25 Å / SU ML: 0.4265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3757
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2685 1198 4.91 %
Rwork0.2476 23197 -
obs0.2486 24395 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 95.97 Å2
Refinement stepCycle: LAST / Resolution: 2.78→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4930 698 62 0 5690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035848
X-RAY DIFFRACTIONf_angle_d0.55758082
X-RAY DIFFRACTIONf_chiral_restr0.0383913
X-RAY DIFFRACTIONf_plane_restr0.0058940
X-RAY DIFFRACTIONf_dihedral_angle_d18.41281068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.890.40691170.38892469X-RAY DIFFRACTION95.28
2.89-3.020.35381250.3332509X-RAY DIFFRACTION99.36
3.02-3.180.33381490.28812549X-RAY DIFFRACTION99.45
3.18-3.380.29751560.29212524X-RAY DIFFRACTION99.7
3.38-3.640.33171450.27842556X-RAY DIFFRACTION99.82
3.64-4.010.26691580.23582557X-RAY DIFFRACTION99.89
4.01-4.590.2255940.21612631X-RAY DIFFRACTION99.89
4.59-5.780.21921400.23042643X-RAY DIFFRACTION99.96
5.78-46.250.25751140.23242759X-RAY DIFFRACTION99.17
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)
11.659359674020.9275340635110.4113946899313.278580082250.8899977378861.32372102687-0.08092266021410.1586608082970.119521887393-0.258627601110.0446854675728-0.0599775322078-0.1074043807510.2239426696590.04476318713920.3249268912760.06479326245160.03555207807480.3660936654080.08578771516940.50185475163833.430340821713.336755007549.0038134665
23.571117918821.522868365863.116226305823.097539241070.9578792300266.00729558466-0.4195533900991.074402973170.302086878643-0.796070391650.4428095644390.108423854123-0.7576714741370.7846839321280.03946517302640.894978032966-0.200527398857-0.06150653539380.8202099633910.08481563217340.79575636927436.400644928129.377610993524.4688997483
31.614938515310.0167004284921-1.212993899192.534708726750.4765457825324.46363894436-0.1981490879580.2977058935610.0735416884898-0.3487974529380.09626041054870.4605130470430.145736514936-0.3006479593980.08450982422180.3754928231650.0141203541813-0.1528670359750.4661622753490.07496205523270.51902843694122.1910913077-1.2331910480737.2460087238
46.553254369182.75947037680.5336365174168.68384569659-0.1253286948165.815984010520.105740792769-0.150453892034-0.726189113805-0.1104297379310.0369758859946-1.56197287686-0.1996551694441.55397782021-0.2397170793460.512379989651-0.01916089882040.1443440905730.759783944875-0.06327224334430.73487072606941.92163413848.7457025620652.0727154508
53.62512458675-3.952767511381.91237433687.504912182520.241987148936.66554637903-0.01230026536851.630323944940.705105755411-0.175367921657-0.178507106468-0.318765291849-0.0238487777697-0.05333149392220.2183723628910.517799096556-0.135186725367-0.1343504420721.042950148860.01588883145710.98338994104138.77417900196.2524039523316.0297306211
67.29387654169-6.355580043323.435933146988.73885762844-0.5997884996273.355561749320.163869931732-0.932892588189-0.590978818546-0.2593001864710.1735359205361.32130159750.255353420877-1.1315329448-0.4165617550780.835545703721-0.293786706803-0.09766128438091.485402285090.4812772671740.98968177652937.583339223910.408856834916.9777527207
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 273 )AA16 - 2731 - 244
22chain 'A' and (resid 274 through 494 )AA274 - 494245 - 445
33chain 'A' and (resid 495 through 704 )AA495 - 704446 - 655
44chain 'B' and (resid 1 through 12 )BB1 - 12
55chain 'C' and (resid 1 through 12 )CC1 - 12
66chain 'D' and (resid 2 through 12 )DD2 - 12

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