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- PDB-8tfg: 1.88A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I -

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Basic information

Entry
Database: PDB / ID: 8tfg
Title1.88A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I
ComponentsDNA topoisomerase 1
KeywordsISOMERASE / EcTopo1 / topoisomerase type I
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 / DNA topoisomerase 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsTan, K. / Tse-Dinh, Y.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM054226 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM139817 United States
CitationJournal: To Be Published
Title: 1.88A CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS TOPOISOMERASE I
Authors: Tan, K. / Tse-Dinh, Y.C.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,29419
Polymers76,1981
Non-polymers1,09618
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.371, 92.876, 139.931
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA topoisomerase 1 / DNA topoisomerase I


Mass: 76197.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: topA, SAMEA2683035_00743 / Plasmid: PET-HIS6-MOCR TEV-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): T7 EXPRESS CRYSTAL / References: UniProt: A0A0E8VY41, DNA topoisomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Sodium Malonate, 20% (w/v) PEG3350

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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 PILATUS 6M / Detector: PIXEL / Date: May 5, 2020
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 68509 / % possible obs: 99.5 % / Observed criterion σ(I): -2 / Redundancy: 4.8 % / Biso Wilson estimate: 33.19 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Χ2: 0.707 / Net I/σ(I): 24.9
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.137 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3289 / CC1/2: 0.501 / CC star: 0.817 / Rpim(I) all: 0.612 / Rrim(I) all: 1.296 / Χ2: 0.63 / % possible all: 96.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D5H

5d5h


Resolution: 1.88→49.49 Å / SU ML: 0.2266 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.1818
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2175 3362 4.96 %
Rwork0.1777 64481 -
obs0.1796 67843 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.14 Å2
Refinement stepCycle: LAST / Resolution: 1.88→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5360 0 72 373 5805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01475600
X-RAY DIFFRACTIONf_angle_d1.25727594
X-RAY DIFFRACTIONf_chiral_restr0.0838847
X-RAY DIFFRACTIONf_plane_restr0.01481008
X-RAY DIFFRACTIONf_dihedral_angle_d6.7664808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.910.37441410.31092515X-RAY DIFFRACTION93.69
1.91-1.940.30531330.26412610X-RAY DIFFRACTION96.99
1.94-1.970.26721380.23382584X-RAY DIFFRACTION97.01
1.97-20.2561330.2152662X-RAY DIFFRACTION98.1
2-2.030.25971430.21172598X-RAY DIFFRACTION98
2.03-2.070.24121420.20972671X-RAY DIFFRACTION98.6
2.07-2.110.22291490.21232653X-RAY DIFFRACTION98.77
2.11-2.150.24681500.21052663X-RAY DIFFRACTION99.19
2.15-2.20.25091420.17462596X-RAY DIFFRACTION97.75
2.2-2.250.23191290.17812707X-RAY DIFFRACTION98.99
2.25-2.310.19011620.17822673X-RAY DIFFRACTION99.06
2.31-2.370.22171190.17682689X-RAY DIFFRACTION99.08
2.37-2.440.23671460.18412679X-RAY DIFFRACTION99.58
2.44-2.520.23561370.18432702X-RAY DIFFRACTION99.47
2.52-2.610.22481580.18182668X-RAY DIFFRACTION99.19
2.61-2.710.24531440.19082675X-RAY DIFFRACTION98.67
2.71-2.840.24231410.19612712X-RAY DIFFRACTION99.79
2.84-2.990.24961380.20032732X-RAY DIFFRACTION99.79
2.99-3.170.2331490.19222715X-RAY DIFFRACTION99.69
3.17-3.420.26231260.19512747X-RAY DIFFRACTION99.17
3.42-3.760.21111300.16792751X-RAY DIFFRACTION99.28
3.76-4.310.18431370.14982768X-RAY DIFFRACTION99.79
4.31-5.430.17631420.14322783X-RAY DIFFRACTION99.12
5.43-49.490.16761330.15882928X-RAY DIFFRACTION99.09
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)
10.746942436311-0.485334841304-0.3790026387481.140335755130.2592145546870.582674485993-0.043030568427-0.01427602929630.04372631602050.295134941531-0.00457572411420.1112255995990.0272068090832-0.1049112061670.05329068261860.264445280166-0.04176669825650.0154052289310.2217940099470.0201953960940.279264307832-37.511531545323.085432268221.8295221057
20.612407189558-0.410805356542-0.6441502973330.898392802370.6981758787651.96294611378-0.136128604994-0.14391470780.001026444637280.2234466306630.196756456759-0.2200638849620.3672802494270.44637109936-0.04936238447780.325526439730.0589642002848-0.05414051369810.293531689163-0.003819488450420.269780810745-7.56711946027-1.0993875748814.6248109544
30.403993353525-0.36726217408-0.1700881304084.158557761671.866675716562.108696688830.05837154688690.225060371204-0.0187963787583-0.253416761518-0.2581963025170.2813786810080.129490515883-0.2527220639570.1945598913390.176573287773-0.0226239394436-0.009404228845790.3499068389060.01235811112780.270265960781-32.692355975610.64099243-6.97727771215
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 17 through 212 )17 - 2121 - 196
22chain 'A' and (resid 213 through 560 )213 - 560197 - 544
33chain 'A' and (resid 561 through 704 )561 - 704545 - 688

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