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- PDB-5d5h: Crystal structure of Mycobacterium tuberculosis Topoisomerase I -

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Basic information

Entry
Database: PDB / ID: 5d5h
TitleCrystal structure of Mycobacterium tuberculosis Topoisomerase I
ComponentsDNA topoisomerase 1
KeywordsISOMERASE / topoisomerase
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
ACETATE ION / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.52 Å
AuthorsTan, K. / Cheng, B. / 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: J.Mol.Biol. / Year: 2016
Title: Insights from the Structure of Mycobacterium tuberculosis Topoisomerase I with a Novel Protein Fold.
Authors: Tan, K. / Cao, N. / Cheng, B. / Joachimiak, A. / Tse-Dinh, Y.C.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5679
Polymers77,8441
Non-polymers7248
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-60 kcal/mol
Surface area32100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.002, 93.149, 140.243
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 / 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) / Strain (production host): T7 Express Crystal / References: UniProt: P9WG49, DNA topoisomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium Sulfate, 0.1M Tris:HCl, 25% (w/v) PEG3350

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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: Mar 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.52→42 Å / Num. all: 28858 / Num. obs: 28858 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 2.52→41.781 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1380 5.02 %Random selection
Rwork0.1737 ---
obs0.1769 27491 94.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→41.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 41 72 5447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085479
X-RAY DIFFRACTIONf_angle_d1.0837438
X-RAY DIFFRACTIONf_dihedral_angle_d14.442037
X-RAY DIFFRACTIONf_chiral_restr0.071829
X-RAY DIFFRACTIONf_plane_restr0.006975
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.61010.33681200.23212265X-RAY DIFFRACTION84
2.6101-2.71460.27281220.20812319X-RAY DIFFRACTION85
2.7146-2.83810.29961450.21242334X-RAY DIFFRACTION87
2.8381-2.98770.28251540.21642549X-RAY DIFFRACTION94
2.9877-3.17480.26851370.21892683X-RAY DIFFRACTION98
3.1748-3.41980.271310.19182739X-RAY DIFFRACTION100
3.4198-3.76380.24391460.17732777X-RAY DIFFRACTION100
3.7638-4.30790.22311470.15012758X-RAY DIFFRACTION100
4.3079-5.42570.20531390.1382800X-RAY DIFFRACTION100
5.4257-41.7870.18871390.1482887X-RAY DIFFRACTION98
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)
10.8915-0.63520.45561.8483-0.63981.4823-0.137-0.02070.01660.34110.09750.0005-0.18-0.16640.0750.2617-0.04980.00910.2871-0.01780.2659.136479.375615.2909
22.1216-1.1540.4962.0901-1.09292.3368-0.07690.1442-0.06760.34330.16780.4916-0.2343-0.5586-0.07840.36580.0680.07150.4312-0.01810.389840.290791.529222.9872
30.9455-0.1829-0.2121.5712-0.38991.2721-0.03310.05740.0250.1383-0.09310.05-0.2202-0.08180.11870.21-0.0108-0.02070.3161-0.03490.249154.074186.53584.0165
40.8814-0.30790.07286.7832-2.80342.80510.0160.39220.0996-0.6391-0.2653-0.489-0.11010.29050.26520.31480.00740.02160.59280.00380.319266.373184.4091-9.4011
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 17 through 287 )
2X-RAY DIFFRACTION2chain 'A' and (resid 288 through 497 )
3X-RAY DIFFRACTION3chain 'A' and (resid 498 through 595 )
4X-RAY DIFFRACTION4chain 'A' and (resid 596 through 704 )

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