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- PDB-8z8y: Crystal structure of CrtAgo/CrtTIR-APAZ complex -

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Basic information

Entry
Database: PDB / ID: 8z8y
TitleCrystal structure of CrtAgo/CrtTIR-APAZ complex
Components
  • Piwi domain-containing protein
  • TIR domain-containing protein
KeywordsDNA BINDING PROTEIN / NADase / 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
Piwi domain-containing protein / TIR domain-containing protein
Similarity search - Component
Biological speciesThermoflavifilum thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 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

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Assembly

Deposited unit
A: Piwi domain-containing protein
B: TIR domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6104
Polymers111,5622
Non-polymers492
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-53 kcal/mol
Surface area44660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.360, 198.360, 184.350
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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: 53256.734 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
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: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 2.0 M Ammonium sulfate, 0.1 M Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.98322 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98322 Å / Relative weight: 1
ReflectionResolution: 3.18→40.61 Å / Num. obs: 36475 / % possible obs: 99.9 % / Redundancy: 39.6 % / Biso Wilson estimate: 117.84 Å2 / Rpim(I) all: 0.052 / Net I/σ(I): 12.5
Reflection shellResolution: 3.18→3.26 Å / Redundancy: 40 % / Num. unique obs: 2646 / Rpim(I) all: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30001.17.1_3660data scaling
HKL-30007.21data reduction
Coot7.21model building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→40.61 Å / SU ML: 0.6113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.1043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2993 1867 5.13 %
Rwork0.2742 34549 -
obs0.2755 36416 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.61 Å2
Refinement stepCycle: LAST / Resolution: 3.18→40.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7761 0 2 7 7770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01337951
X-RAY DIFFRACTIONf_angle_d1.645810753
X-RAY DIFFRACTIONf_chiral_restr0.08011159
X-RAY DIFFRACTIONf_plane_restr0.0081371
X-RAY DIFFRACTIONf_dihedral_angle_d25.58312971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.270.46661650.42572577X-RAY DIFFRACTION99.96
3.27-3.360.43681130.39132652X-RAY DIFFRACTION100
3.36-3.470.43581340.37722612X-RAY DIFFRACTION99.96
3.47-3.590.37111730.3522564X-RAY DIFFRACTION100
3.59-3.740.41461400.34962641X-RAY DIFFRACTION100
3.74-3.910.35551400.33172622X-RAY DIFFRACTION100
3.91-4.110.40831390.3262627X-RAY DIFFRACTION100
4.11-4.370.32331190.27832676X-RAY DIFFRACTION99.96
4.37-4.710.27791580.2692638X-RAY DIFFRACTION100
4.71-5.180.31321290.26152670X-RAY DIFFRACTION100
5.18-5.930.31171560.2722678X-RAY DIFFRACTION99.93
5.93-7.460.26251460.26552732X-RAY DIFFRACTION100
7.46-40.610.20871550.21022860X-RAY DIFFRACTION99.24

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