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- PDB-8z96: Crystal structure of CrtAgo/TIR-APAZ in complex with guide DNA an... -

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Basic information

Entry
Database: PDB / ID: 8z96
TitleCrystal structure of CrtAgo/TIR-APAZ in complex with guide DNA and 21-nt target DNA
Components
  • DNA (5'-D(*CP*TP*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 / NADase / DNA / Complex / 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: 3.36 Å
AuthorsHu, R. / Chen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022047 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
DepositionApr 22, 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(*CP*TP*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)121,1105
Polymers121,0864
Non-polymers241
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10870 Å2
ΔGint-81 kcal/mol
Surface area44310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.574, 133.574, 167.258
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
Components on special symmetry positions
IDModelComponents
11A-604-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#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

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DNA chain , 2 types, 2 molecules CD

#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(*CP*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')


Mass: 6286.101 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermoflavifilum thermophilum (bacteria)

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Non-polymers , 2 types, 26 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.56 Å3/Da / Density % sol: 65.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% v/v Tacsimate, pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole, pH 7.0, 8% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.94138 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94138 Å / Relative weight: 1
ReflectionResolution: 3.36→50 Å / Num. obs: 25189 / % possible obs: 100 % / Redundancy: 17.3 % / Biso Wilson estimate: 51.11 Å2 / Rpim(I) all: 0.052 / Net I/σ(I): 14.8
Reflection shellResolution: 3.36→3.42 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 3 / Num. unique obs: 1220 / Rpim(I) all: 0.276 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data scaling
HKL-30007.21data reduction
Coot0.7.2.1model building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→20.68 Å / SU ML: 0.4364 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 28.5046
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2872 1049 4.71 %
Rwork0.247 21215 -
obs0.2489 22264 89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.48 Å2
Refinement stepCycle: LAST / Resolution: 3.36→20.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7279 858 1 25 8163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01528422
X-RAY DIFFRACTIONf_angle_d1.753111574
X-RAY DIFFRACTIONf_chiral_restr0.09841257
X-RAY DIFFRACTIONf_plane_restr0.0071323
X-RAY DIFFRACTIONf_dihedral_angle_d28.74573193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.530.3634570.30411440X-RAY DIFFRACTION42.65
3.54-3.760.33451440.27252686X-RAY DIFFRACTION79.9
3.76-4.040.29051690.26073368X-RAY DIFFRACTION99.94
4.04-4.450.26391610.22893381X-RAY DIFFRACTION100
4.45-5.080.251760.22133385X-RAY DIFFRACTION99.97
5.08-6.370.30761510.26343448X-RAY DIFFRACTION100
6.37-20.680.28121910.23633507X-RAY DIFFRACTION99.49

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