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- PDB-7ygl: Crystal Structure of the ring nuclease Sso2081 from Saccharolobus... -

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Basic information

Entry
Database: PDB / ID: 7ygl
TitleCrystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with A4>p cleavage intermediate
Components
  • CRISPR system ring nuclease SSO2081
  • RNA (5'-R(*AP*AP*AP*(A23))-3')
KeywordsHYDROLASE / Sso2081 S11A mutant / ring nuclease / cyclic-tetraadenylates(cA4) / protein-cA4 complex
Function / homologyCRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / Restriction endonuclease type II-like / Lyases; Phosphorus-oxygen lyases / defense response to virus / lyase activity / cytoplasm / RNA / CRISPR system ring nuclease SSO2081
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLin, Z. / Du, L. / Luo, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Molecular basis of stepwise cyclic tetra-adenylate cleavage by the type III CRISPR ring nuclease Crn1/Sso2081.
Authors: Du, L. / Zhang, D. / Luo, Z. / Lin, Z.
History
DepositionJul 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 29, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR system ring nuclease SSO2081
B: CRISPR system ring nuclease SSO2081
C: RNA (5'-R(*AP*AP*AP*(A23))-3')


Theoretical massNumber of molelcules
Total (without water)42,9263
Polymers42,9263
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-9 kcal/mol
Surface area15850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.510, 39.144, 74.088
Angle α, β, γ (deg.)90.000, 105.178, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR system ring nuclease SSO2081


Mass: 20796.131 Da / Num. of mol.: 2 / Mutation: S11A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus P2 (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO2081 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q7LYJ6, Lyases; Phosphorus-oxygen lyases
#2: RNA chain RNA (5'-R(*AP*AP*AP*(A23))-3')


Mass: 1333.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Sodium acetate trihydrate, pH 5.0, 20% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 13097 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.043 / Net I/σ(I): 32.22
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.86 / Num. unique obs: 1285 / CC1/2: 0.897 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data scaling
MOLREPphasing
Cootmodel building
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YHL

7yhl


Resolution: 2.5→28.91 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.923 / SU B: 17.303 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R: 1.454 / ESU R Free: 0.347
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 683 5.218 %RANDOM
Rwork0.2578 12407 --
all0.259 ---
obs-13090 98.785 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 114.148 Å2
Baniso -1Baniso -2Baniso -3
1--3.444 Å20 Å20.787 Å2
2--7.902 Å2-0 Å2
3----4.259 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2856 88 0 6 2950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122995
X-RAY DIFFRACTIONr_bond_other_d0.0090.0162868
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.6454043
X-RAY DIFFRACTIONr_angle_other_deg0.6261.5646703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4375360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.9531019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69310586
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.4710123
X-RAY DIFFRACTIONr_chiral_restr0.0820.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02528
X-RAY DIFFRACTIONr_nbd_refined0.1550.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.22826
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21399
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1030.216
X-RAY DIFFRACTIONr_nbd_other0.2340.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2590.24
X-RAY DIFFRACTIONr_mcbond_it18.54511.2561446
X-RAY DIFFRACTIONr_mcbond_other18.54411.2561446
X-RAY DIFFRACTIONr_mcangle_it24.18316.8411804
X-RAY DIFFRACTIONr_mcangle_other24.17716.8431805
X-RAY DIFFRACTIONr_scbond_it18.53212.0781549
X-RAY DIFFRACTIONr_scbond_other18.5312.0791549
X-RAY DIFFRACTIONr_scangle_it25.29317.6842239
X-RAY DIFFRACTIONr_scangle_other25.28717.6832240
X-RAY DIFFRACTIONr_lrange_it30.288218.49911623
X-RAY DIFFRACTIONr_lrange_other30.287218.48511624
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.502-2.5670.406600.402820X-RAY DIFFRACTION90.535
2.567-2.6360.438460.395874X-RAY DIFFRACTION99.1379
2.636-2.7120.47400.385884X-RAY DIFFRACTION100
2.712-2.7950.349600.37839X-RAY DIFFRACTION99.4469
2.795-2.8860.365490.342781X-RAY DIFFRACTION99.2823
2.886-2.9860.394360.287807X-RAY DIFFRACTION100
2.986-3.0970.308440.279741X-RAY DIFFRACTION100
3.097-3.2220.396310.317762X-RAY DIFFRACTION100
3.222-3.3640.268240.296705X-RAY DIFFRACTION99.863
3.364-3.5250.381330.308687X-RAY DIFFRACTION99.8613
3.525-3.7130.32380.284629X-RAY DIFFRACTION98.2327
3.713-3.9340.242380.255610X-RAY DIFFRACTION100
3.934-4.20.333260.261565X-RAY DIFFRACTION100
4.2-4.5290.227320.255547X-RAY DIFFRACTION100
4.529-4.9490.347270.231509X-RAY DIFFRACTION99.8138
4.949-5.5130.218160.26445X-RAY DIFFRACTION97.2574
5.513-6.3280.246280.245404X-RAY DIFFRACTION100
6.328-7.6590.246260.243349X-RAY DIFFRACTION100
7.659-10.470.114130.172278X-RAY DIFFRACTION98.3108
10.47-28.910.324160.213171X-RAY DIFFRACTION96.8912

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