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- PDB-8z92: Crystal structure of CrtAgo/TIR-APAZ in complex with guide DNA an... -

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Basic information

Entry
Database: PDB / ID: 8z92
TitleCrystal structure of CrtAgo/TIR-APAZ in complex with guide DNA and 16-nt target DNA
Components
  • DNA (5'-D(*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: 3.85 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
B: Piwi domain-containing protein
E: TIR domain-containing protein
G: TIR domain-containing protein
A: Piwi domain-containing protein
D: DNA (5'-D(*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
F: 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')
H: DNA (5'-D(*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
I: 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')


Theoretical massNumber of molelcules
Total (without water)239,1238
Polymers239,1238
Non-polymers00
Water00
1
B: Piwi domain-containing protein
E: TIR domain-containing protein
D: DNA (5'-D(*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
F: 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')


Theoretical massNumber of molelcules
Total (without water)119,5624
Polymers119,5624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-60 kcal/mol
Surface area45950 Å2
MethodPISA
2
G: TIR domain-containing protein
A: Piwi domain-containing protein
H: DNA (5'-D(*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')
I: 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')


Theoretical massNumber of molelcules
Total (without water)119,5624
Polymers119,5624
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-61 kcal/mol
Surface area44610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.179, 287.266, 111.766
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETPROPRO(chain 'A' and (resid 1 through 153 or resid 198 or resid 203 through 507))AD1 - 1531 - 153
121LYSLYSLYSLYS(chain 'A' and (resid 1 through 153 or resid 198 or resid 203 through 507))AD198198
131ASPASPILEILE(chain 'A' and (resid 1 through 153 or resid 198 or resid 203 through 507))AD203 - 507203 - 507
241METMETPROPRO(chain 'B' and (resid 1 through 153 or resid 165 or resid 203 through 507))BA1 - 1531 - 153
251LYSLYSLYSLYS(chain 'B' and (resid 1 through 153 or resid 165 or resid 203 through 507))BA165165
261ASPASPILEILE(chain 'B' and (resid 1 through 153 or resid 165 or resid 203 through 507))BA203 - 507203 - 507
172DCDCDTDTchain 'D'DE1 - 161 - 16
282DCDCDTDTchain 'H'HG1 - 161 - 16
193METMETPROPROchain 'E'EB1 - 4191 - 419
2103METMETPROPRO(chain 'G' and (resid 1 through 158 or (resid 159...GC1 - 4191 - 419
1114DTDTDTDTchain 'F'FF0 - 201 - 21
2124DTDTDTDTchain 'I'IH0 - 201 - 21

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein Piwi domain-containing protein


Mass: 58304.848 Da / Num. of mol.: 2
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.: 2
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(*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*AP*T)-3')


Mass: 4762.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermoflavifilum thermophilum (bacteria)
#4: 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.: 2 / Source method: obtained synthetically / Source: (synth.) Thermoflavifilum thermophilum (bacteria)
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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS propane, pH 9.0 and 8% w/v Polyethylene glycol 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 3.85→50 Å / Num. obs: 38276 / % possible obs: 99.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 43.77 Å2 / Rpim(I) all: 0.17 / Net I/σ(I): 3.5
Reflection shellResolution: 3.85→3.92 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.33 / Num. unique obs: 1544 / Rpim(I) all: 0.518 / % possible all: 99.4

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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: 3.85→46.25 Å / SU ML: 0.537 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.8771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2648 3147 8.22 %
Rwork0.2468 35129 -
obs0.2483 38276 64.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.47 Å2
Refinement stepCycle: LAST / Resolution: 3.85→46.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14536 1514 0 0 16050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004316597
X-RAY DIFFRACTIONf_angle_d0.807222760
X-RAY DIFFRACTIONf_chiral_restr0.04872459
X-RAY DIFFRACTIONf_plane_restr0.00542630
X-RAY DIFFRACTIONf_dihedral_angle_d22.45276294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.85-3.910.248720.334514X-RAY DIFFRACTION0.6
3.91-3.980.280660.301766X-RAY DIFFRACTION2.69
3.98-4.050.3236220.3109240X-RAY DIFFRACTION9.86
4.05-4.120.341400.2444459X-RAY DIFFRACTION18.63
4.12-4.20.239570.2584638X-RAY DIFFRACTION26.16
4.2-4.280.2717760.2572838X-RAY DIFFRACTION33.76
4.28-4.380.2978940.26521045X-RAY DIFFRACTION42.55
4.38-4.480.25731100.2591246X-RAY DIFFRACTION50.43
4.48-4.590.27811200.26021426X-RAY DIFFRACTION57.92
4.59-4.720.27961400.25461598X-RAY DIFFRACTION63.78
4.72-4.850.25451610.26241795X-RAY DIFFRACTION72.55
4.85-5.010.25741820.25292011X-RAY DIFFRACTION82.69
5.01-5.190.30842010.26782176X-RAY DIFFRACTION88.33
5.19-5.40.30562030.26822273X-RAY DIFFRACTION92.94
5.4-5.640.30762250.27852437X-RAY DIFFRACTION97.54
5.64-5.940.27512210.26742401X-RAY DIFFRACTION98.09
5.94-6.310.27192160.2822454X-RAY DIFFRACTION98.6
6.31-6.80.32772120.27492394X-RAY DIFFRACTION98.04
6.8-7.480.26432180.25652441X-RAY DIFFRACTION98.34
7.48-8.550.2592130.22632439X-RAY DIFFRACTION98.99
8.55-10.750.18942220.17912412X-RAY DIFFRACTION98.8
10.76-46.250.21042060.19462326X-RAY DIFFRACTION93.6

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