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- PDB-9l9w: Structure of SPARTA in complex with guide DNA and a 19nt target DNA -

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Basic information

Entry
Database: PDB / ID: 9l9w
TitleStructure of SPARTA in complex with guide DNA and a 19nt target DNA
Components
  • DNA (5'-D(*T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
  • DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
  • Piwi domain-containing protein
  • TIR domain-containing protein
KeywordsDNA BINDING PROTEIN/DNA / Ago / TIR-APAZ / DNA / NADase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


nucleic acid binding / signal transduction / metal ion binding
Similarity search - Function
TIR domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Piwi domain-containing protein / TIR domain-containing protein
Similarity search - Component
Biological speciesThermoflavifilum thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.87 Å
AuthorsHu, R. / Guo, C. / Liu, X. / Chen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2025
Title: Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system.
Authors: Hu, R. / Guo, C. / Liu, X. / Lin, Y. / Yang, Z. / Li, Z. / Yang, Y. / Ma, E. / Li, Y. / Chen, J. / Liu, L.
History
DepositionDec 31, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Piwi domain-containing protein
B: TIR domain-containing protein
C: DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')
D: DNA (5'-D(*T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,8215
Polymers120,7964
Non-polymers241
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10760 Å2
ΔGint-77 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.189, 136.189, 174.919
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Piwi domain-containing protein


Mass: 58304.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoflavifilum thermophilum (bacteria)
Gene: SAMN05660895_1671 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I7NFD7
#2: Protein TIR domain-containing protein


Mass: 49906.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoflavifilum thermophilum (bacteria)
Gene: SAMN05660895_1670 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I7NFG5
#3: DNA chain DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3')


Mass: 6588.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermoflavifilum thermophilum (bacteria)
#4: DNA chain DNA (5'-D(*T*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')


Mass: 5996.919 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermoflavifilum thermophilum (bacteria)
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
Has protein modificationN

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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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BICINE, pH=8.5, 4.4% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 5.87→39.32 Å / Num. obs: 5233 / % possible obs: 99.6 % / Redundancy: 17.6 % / Biso Wilson estimate: 295.22 Å2 / Rpim(I) all: 0.059 / Net I/σ(I): 7.5
Reflection shellResolution: 5.87→6.02 Å / Num. unique obs: 371 / Rpim(I) all: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
Coot0.7.2.1model building
PHENIX1.17.1_3660refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 5.87→39.31 Å / SU ML: 1.0505 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2884 265 5.06 %
Rwork0.261 4968 -
obs0.2625 5233 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 317.2 Å2
Refinement stepCycle: LAST / Resolution: 5.87→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7279 819 1 0 8099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01578379
X-RAY DIFFRACTIONf_angle_d1.5211508
X-RAY DIFFRACTIONf_chiral_restr0.06871249
X-RAY DIFFRACTIONf_plane_restr0.00891321
X-RAY DIFFRACTIONf_dihedral_angle_d28.10143173
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.87-7.380.39231370.32082439X-RAY DIFFRACTION99.31
7.39-39.310.25551280.2442529X-RAY DIFFRACTION98.55

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