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

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Basic information

Entry
Database: PDB / ID: 7ygh
TitleCrystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with cyclic-tetraadenylate (cA4)
Components
  • CRISPR system ring nuclease SSO2081
  • RNA (5'-R(P*AP*AP*AP*A)-3')
KeywordsHYDROLASE / Sso2081 / 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: 3.11 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)42,8963
Polymers42,8963
Non-polymers00
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-11 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.052, 38.837, 72.965
Angle α, β, γ (deg.)90.000, 105.798, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR system ring nuclease SSO2081


Mass: 20812.131 Da / Num. of mol.: 2
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(P*AP*AP*AP*A)-3')


Mass: 1271.866 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.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Sodium acetate trihydrate, pH 5.0, 22% w/v Polyethylene glycol monomethyl ether 550, 5% w/v n-Dodecyl-B-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Mar 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.11→50 Å / Num. obs: 6715 / % possible obs: 99.57 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.84
Reflection shellResolution: 3.11→3.22 Å / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.88 / Num. unique obs: 665 / CC1/2: 0.602 / % possible all: 100

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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: 3.11→28.556 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.242 / SU B: 27.222 / SU ML: 0.467 / Average fsc free: 0.9427 / Average fsc work: 0.9503 / Cross valid method: THROUGHOUT / ESU R Free: 0.555
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2584 328 4.888 %RANDOM
Rwork0.2379 6382 --
all0.239 ---
obs-6710 99.54 %-
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: 136.267 Å2
Baniso -1Baniso -2Baniso -3
1--1.611 Å2-0 Å23.216 Å2
2---0.998 Å20 Å2
3---0.681 Å2
Refinement stepCycle: LAST / Resolution: 3.11→28.556 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2850 88 0 1 2939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122989
X-RAY DIFFRACTIONr_bond_other_d0.0080.0162860
X-RAY DIFFRACTIONr_angle_refined_deg1.711.6444035
X-RAY DIFFRACTIONr_angle_other_deg0.651.5646683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0485360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.9481019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19110584
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.52610121
X-RAY DIFFRACTIONr_chiral_restr0.0830.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023248
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02528
X-RAY DIFFRACTIONr_nbd_refined0.1690.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.22911
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21415
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.220.27
X-RAY DIFFRACTIONr_nbd_other0.2310.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2840.23
X-RAY DIFFRACTIONr_mcbond_it21.76813.5561446
X-RAY DIFFRACTIONr_mcbond_other21.76813.5571446
X-RAY DIFFRACTIONr_mcangle_it30.39820.2061804
X-RAY DIFFRACTIONr_mcangle_other30.39120.2051805
X-RAY DIFFRACTIONr_scbond_it19.82514.3651543
X-RAY DIFFRACTIONr_scbond_other19.82114.3661543
X-RAY DIFFRACTIONr_scangle_it29.12221.0942231
X-RAY DIFFRACTIONr_scangle_other29.11621.0922232
X-RAY DIFFRACTIONr_lrange_it38.41254.99611665
X-RAY DIFFRACTIONr_lrange_other38.409254.9811666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.11-3.1890.383230.3374480.3394870.9140.91996.71460.305
3.189-3.2760.387250.3394380.3424630.9040.9151000.311
3.276-3.3690.328200.3334370.3334570.9240.9221000.306
3.369-3.4720.252170.34350.2984530.960.93999.77930.265
3.472-3.5840.387200.284220.2844420.8960.9481000.242
3.584-3.7070.282240.2643940.2654180.9570.9561000.231
3.707-3.8450.25170.2513940.2514110.9650.9571000.222
3.845-3.9990.268230.243550.2423780.9620.9621000.217
3.999-4.1730.261160.2593530.2593690.970.9591000.24
4.173-4.3720.264190.283600.2793790.9570.9491000.261
4.372-4.6020.308150.2543250.2563400.9290.9591000.247
4.602-4.8740.195170.2283290.2263460.9590.9661000.226
4.874-5.1990.276200.2522780.2542980.9550.9591000.247
5.199-5.60.396120.2372940.2423060.8930.9661000.242
5.6-6.1120.368150.2682350.2742520.9370.95999.20630.274
6.112-6.7940.189160.2472370.2432530.9770.9591000.268
6.794-7.7720.21590.2132160.2132250.9650.9691000.232
7.772-9.3470.09370.1551850.1521920.9940.9861000.184
9.347-12.5630.23760.151470.1531530.9670.9831000.206
12.563-28.5560.28170.2271000.2311080.9280.96799.07410.297

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