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- PDB-5uj1: Crystal structure of Mycobacterium tuberculosis Topoisomerase I a... -

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Basic information

Entry
Database: PDB / ID: 5uj1
TitleCrystal structure of Mycobacterium tuberculosis Topoisomerase I at 2.15A resolution limit
ComponentsDNA topoisomerase 1
KeywordsISOMERASE / Topoisomerase I / Mycobacterium tuberculosis
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 / metal ion 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
DNA topoisomerase 1 / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.153 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 16, 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 1.5Apr 13, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.6Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9402
Polymers77,8441
Non-polymers961
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area31520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.783, 93.588, 140.571
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: 77843.500 Da / Num. of mol.: 1 / Fragment: UNP residues 63-768
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, EC: 5.99.1.2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium sodium tartrate, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2016 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.15→47.233 Å / Num. obs: 46076 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.044 / Χ2: 0.791 / Net I/σ(I): 17.4
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2263 / CC1/2: 0.734 / Rpim(I) all: 0.391 / Χ2: 0.636 / % possible all: 99

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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: 2.153→47.233 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2105 2310 5.02 %random
Rwork0.1682 ---
obs0.1704 46007 99.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.153→47.233 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 5 301 5616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075435
X-RAY DIFFRACTIONf_angle_d0.8047389
X-RAY DIFFRACTIONf_dihedral_angle_d19.0943298
X-RAY DIFFRACTIONf_chiral_restr0.05829
X-RAY DIFFRACTIONf_plane_restr0.006974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1535-2.19740.28351260.23582465X-RAY DIFFRACTION96
2.1974-2.24520.29191320.21962503X-RAY DIFFRACTION100
2.2452-2.29740.24781500.20282533X-RAY DIFFRACTION99
2.2974-2.35490.23251290.20062556X-RAY DIFFRACTION100
2.3549-2.41850.26421250.18952541X-RAY DIFFRACTION100
2.4185-2.48970.24721310.19642552X-RAY DIFFRACTION100
2.4897-2.570.29791310.1982563X-RAY DIFFRACTION100
2.57-2.66190.25191300.1942576X-RAY DIFFRACTION100
2.6619-2.76850.23591380.19322557X-RAY DIFFRACTION100
2.7685-2.89440.23761310.19052538X-RAY DIFFRACTION99
2.8944-3.0470.25451330.19172574X-RAY DIFFRACTION100
3.047-3.23790.25741400.18242580X-RAY DIFFRACTION99
3.2379-3.48780.22721570.18212549X-RAY DIFFRACTION100
3.4878-3.83870.19181380.15732589X-RAY DIFFRACTION99
3.8387-4.39380.17381440.13332623X-RAY DIFFRACTION100
4.3938-5.53430.17011300.13022624X-RAY DIFFRACTION99
5.5343-47.24470.15951450.15692774X-RAY DIFFRACTION99
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)
11.0118-0.4048-0.40811.09410.2030.821-0.0799-0.0620.00760.3129-0.01240.16050.0552-0.14280.10410.2821-0.04750.02790.2286-0.00440.2687-5.418423.317121.8218
20.647-0.2337-0.05581.0520.56342.366-0.09050.0161-0.13960.15110.131-0.30420.38960.5763-0.02230.34080.06330.01730.39210.02040.398824.0089-1.393514.684
30.8569-0.01740.066.37133.1153.18470.02790.349-0.124-0.3936-0.26140.3540.1121-0.20760.21570.21120.00050.0030.44-0.00640.2954-0.332511.0829-6.9935
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 18 through 212 )
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 560 )
3X-RAY DIFFRACTION3chain 'A' and (resid 561 through 704 )

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