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- PDB-5ujy: The structure of Mycobacterium tuberculosis topoisomerase I from ... -

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Basic information

Entry
Database: PDB / ID: 5ujy
TitleThe structure of Mycobacterium tuberculosis topoisomerase I from the 2nd crystal form
ComponentsDNA topoisomerase 1Topoisomerase
KeywordsISOMERASE / DNA Topoisomerase I
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 / metal ion 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. / 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 / Topoisomerase I; domain 3 / 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
DNA topoisomerase 1 / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCao, N. / Tan, K. / Tse-Dinh, Y.C.
Funding support United States, 2items
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
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
DepositionJan 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Jul 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 1.3Sep 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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 topoisomerase 1


Theoretical massNumber of molelcules
Total (without water)155,6872
Polymers155,6872
Non-polymers00
Water84747
1
A: DNA topoisomerase 1


Theoretical massNumber of molelcules
Total (without water)77,8441
Polymers77,8441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA topoisomerase 1


Theoretical massNumber of molelcules
Total (without water)77,8441
Polymers77,8441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)170.573, 64.412, 169.345
Angle α, β, γ (deg.)90.00, 112.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 77843.500 Da / Num. of mol.: 2
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: PET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL
References: UniProt: A0A0E8VY41, UniProt: P9WG49*PLUS, DNA topoisomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES:NaCl, 16 % (w/v) PEG 8000, 8 % (v/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 8, 2016 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.7→42.258 Å / Num. obs: 45105 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 50.9 Å2 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.062 / Χ2: 1.686 / Net I/σ(I): 14.3
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.843 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2195 / CC1/2: 0.524 / Rpim(I) all: 0.391 / Χ2: 0.535 / % possible all: 95.7

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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: 5D5H

5d5h


Resolution: 2.7→42.258 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.73
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 2210 4.9 %random
Rwork0.1983 ---
obs0.2004 45061 95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→42.258 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10579 0 0 47 10626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310792
X-RAY DIFFRACTIONf_angle_d0.50114665
X-RAY DIFFRACTIONf_dihedral_angle_d19.0666557
X-RAY DIFFRACTIONf_chiral_restr0.041654
X-RAY DIFFRACTIONf_plane_restr0.0041928
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.75890.3244760.24451654X-RAY DIFFRACTION59
2.7589-2.8230.28721850.24662723X-RAY DIFFRACTION99
2.823-2.89360.32031240.2432771X-RAY DIFFRACTION100
2.8936-2.97180.30581600.23612755X-RAY DIFFRACTION100
2.9718-3.05930.29871440.24612814X-RAY DIFFRACTION100
3.0593-3.1580.32321380.24442774X-RAY DIFFRACTION100
3.158-3.27080.37831340.24962772X-RAY DIFFRACTION100
3.2708-3.40170.33321410.23942810X-RAY DIFFRACTION100
3.4017-3.55640.25581510.22492774X-RAY DIFFRACTION100
3.5564-3.74380.33391230.27652374X-RAY DIFFRACTION86
3.7438-3.97820.23751520.20462627X-RAY DIFFRACTION94
3.9782-4.28510.21491390.16682761X-RAY DIFFRACTION98
4.2851-4.71590.17741310.15052788X-RAY DIFFRACTION100
4.7159-5.39710.18741440.15342834X-RAY DIFFRACTION99
5.3971-6.79520.20621300.17932820X-RAY DIFFRACTION99
6.7952-42.26360.16641380.15672800X-RAY DIFFRACTION95
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)
11.48721.36760.47751.4319-0.27291.06420.2452-0.5202-0.36760.5676-0.3714-0.41090.13670.22070.01580.5701-0.0665-0.1010.6860.14370.4878-25.7339-49.60924.2065
21.65450.636-0.60182.7858-0.69581.66960.0609-0.0513-0.1522-0.2823-0.10410.00510.1479-0.12820.04310.32620.02480.050.42820.00560.3086-35.0858-44.2809-1.8173
30.8470.06640.66271.2784-0.8042.72420.0811-0.01630.1923-0.1723-0.0824-0.2219-0.32190.0664-0.04370.43510.0720.19030.38260.01690.4732-16.4633-15.695-11.2924
42.34730.69680.08723.1068-0.59463.82860.3617-0.5547-0.15750.3495-0.1938-0.1985-0.16590.4493-0.02150.3826-0.1044-0.07950.5416-0.03560.4257-9.7854-23.448316.0914
50.85330.3756-0.2911.0046-0.04561.02420.10830.02190.0825-0.1118-0.1047-0.1396-0.25680.0540.02240.40950.02440.06520.35190.04990.3797-22.0334-23.907-5.1868
61.68470.3394-0.78590.374-1.12413.7161-0.18150.5859-0.0911-0.89760.09160.5990.5121-0.7283-0.08030.9835-0.1594-0.15550.5549-0.01840.3865-43.3041-43.9715-14.4191
71.45650.6151-0.04681.16621.49134.55530.41940.9916-1.0404-0.58880.0382-0.14891.19170.1638-0.0991.47610.0934-0.12020.9012-0.25230.7219-29.5751-47.0628-31.4194
82.88920.5608-1.81921.5187-0.54021.95190.0112-0.24480.21280.753-0.07990.4112-0.1634-0.2628-0.05410.61240.01550.16340.4503-0.07450.4444-26.6226-4.9594-54.571
90.70.13230.38192.21210.72361.38050.113-0.0287-0.18190.0446-0.19590.85910.2836-0.2760.08980.4107-0.0022-0.07720.3813-0.0140.7077-35.6082-33.4711-79.2481
100.64860.59470.91750.92920.53880.86520.08-0.0626-0.1695-0.419-0.32071.02530.3768-0.31340.14710.6736-0.0445-0.18910.4915-0.1471.0371-40.9137-41.9382-88.6648
111.31720.2378-0.12892.61660.5782.06510.05420.0243-0.059-0.0275-0.0460.1748-0.1081-0.0647-0.05440.285-0.0039-0.01930.2375-0.00720.3216-18.4839-17.0373-78.3835
122.13830.29570.01181.21770.15542.9948-0.02371.07020.3174-0.7159-0.07470.1839-0.58320.51820.11390.923-0.0105-0.05790.60380.08170.4966-15.5725-10.9878-99.9452
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 157 )
2X-RAY DIFFRACTION2chain 'A' and (resid 158 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 351 )
4X-RAY DIFFRACTION4chain 'A' and (resid 352 through 415 )
5X-RAY DIFFRACTION5chain 'A' and (resid 416 through 609 )
6X-RAY DIFFRACTION6chain 'A' and (resid 610 through 662 )
7X-RAY DIFFRACTION7chain 'A' and (resid 663 through 702 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 142 )
9X-RAY DIFFRACTION9chain 'B' and (resid 143 through 460 )
10X-RAY DIFFRACTION10chain 'B' and (resid 461 through 528 )
11X-RAY DIFFRACTION11chain 'B' and (resid 529 through 609 )
12X-RAY DIFFRACTION12chain 'B' and (resid 610 through 704 )

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