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- PDB-6ozw: Crystal structure of the 65-kilodalton amino-terminal fragment of... -

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Basic information

Entry
Database: PDB / ID: 6ozw
TitleCrystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from Streptococcus mutans
ComponentsDNA topoisomerase 1
KeywordsISOMERASE / DNA BINDING PROTEIN / topoisomerase / supercoiled
Function / homology
Function and homology information


DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / chromosome / DNA binding / metal ion binding
Similarity search - Function
DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / 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 ...DNA topoisomerase, type IA, zn finger / Topoisomerase DNA binding C4 zinc finger / 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 / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DNA topoisomerase 1
Similarity search - Component
Biological speciesStreptococcus mutans serotype c (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.063 Å
AuthorsJones, J.A. / Hevener, K.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20 GM103408 United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Crystal structure of the 65-kilodalton amino-terminal fragment of DNA topoisomerase I from the gram-positive model organism Streptococcus mutans.
Authors: Jones, J.A. / Hevener, K.E.
History
DepositionMay 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)68,57421
Polymers67,7831
Non-polymers79020
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.581, 98.366, 72.706
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA topoisomerase 1 / DNA topoisomerase I


Mass: 67783.391 Da / Num. of mol.: 1 / Fragment: residues 1-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans serotype c (strain ATCC 700610 / UA159) (bacteria)
Strain: ATCC 700610 / UA159 / Gene: topA, SMU_1002 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8DUD3, DNA topoisomerase (ATP-hydrolysing)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.57 Å3/Da / Density % sol: 52.17 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 4.6 mg mL-1 in a 3uL:3uL 1:1 ratio protein to condition, crystallization condition 0.2 M magnesium formate dihydrate, 25% w/v PEG 3350 at 277.15 K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 39033 / % possible obs: 97.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.78 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Χ2: 0.941 / Net I/σ(I): 7.3 / Num. measured all: 254919
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.15.10.94416550.690.4411.0470.88283.3
2.1-2.135.70.77617600.8320.3390.8490.85990.2
2.13-2.176.30.68418480.8820.2820.7410.89994.1
2.17-2.226.40.60418870.8920.2490.6550.90295.9
2.22-2.276.40.51319320.9420.2120.5560.88497.9
2.27-2.326.50.45919490.9390.1910.4980.92298.6
2.32-2.386.40.39319370.9590.1670.4280.90698.9
2.38-2.446.60.35319720.9660.1470.3830.90799.1
2.44-2.516.60.29719630.9780.1240.3220.92599
2.51-2.670.24719600.9790.0990.2660.93498.9
2.6-2.696.90.20219690.9870.0820.2180.93299.5
2.69-2.86.80.16219810.990.0660.1761.01299.5
2.8-2.926.50.13219610.9930.0550.1441.01699.2
2.92-3.086.60.10720000.9950.0450.1161.04499.5
3.08-3.2770.08119810.9970.0320.0871.01899.5
3.27-3.526.90.06319940.9970.0250.0681.03199.6
3.52-3.886.60.05620110.9970.0230.0611.10399.8
3.88-4.446.80.04620290.9980.0190.051.00999.9
4.44-5.596.60.04320630.9980.0180.0470.854100
5.59-506.40.03721810.9980.0160.0410.72100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ECL

1ecl


Resolution: 2.063→49.183 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.04
RfactorNum. reflection% reflection
Rfree0.2677 1651 5.05 %
Rwork0.2003 --
obs0.2038 32714 82.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.86 Å2 / Biso mean: 33.1822 Å2 / Biso min: 9.72 Å2
Refinement stepCycle: final / Resolution: 2.063→49.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 48 313 4700
Biso mean--46.11 32.35 -
Num. residues----538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084447
X-RAY DIFFRACTIONf_angle_d0.9155963
X-RAY DIFFRACTIONf_chiral_restr0.052658
X-RAY DIFFRACTIONf_plane_restr0.005761
X-RAY DIFFRACTIONf_dihedral_angle_d2.9032731
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0626-2.12330.3697490.22921043109234
2.1233-2.19180.3128770.22531518159549
2.1918-2.27020.3003880.23251863195159
2.2702-2.36110.2926920.23642154224669
2.3611-2.46850.28631470.24682495264281
2.4685-2.59870.35681540.25442974312894
2.5987-2.76150.35131690.24113040320999
2.7615-2.97470.29761810.2493117329899
2.9747-3.2740.27751550.23023157331299
3.274-3.74760.2762000.195131233323100
3.7476-4.72090.23831730.153732173390100
4.7209-49.1970.17971660.151633623528100

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