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

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Basic information

Entry
Database: PDB / ID: 7yhl
TitleCrystal Structure of the ring nuclease Sso2081 from Saccharolobus solfataricus in complex with free phosphate
ComponentsCRISPR system ring nuclease SSO2081
KeywordsHYDROLASE / Sso2081 / ring nuclease / wild type / free phosphate
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 / PHOSPHATE ION / CRISPR system ring nuclease SSO2081
Function and homology information
Biological speciesSaccharolobus solfataricus P2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 13, 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 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0524
Polymers40,8622
Non-polymers1902
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-26 kcal/mol
Surface area15550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.027, 38.376, 69.798
Angle α, β, γ (deg.)90.000, 106.412, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR system ring nuclease SSO2081


Mass: 20431.061 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) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: Q7LYJ6, Lyases; Phosphorus-oxygen lyases
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.1 M Sodium acetate trihydrate, pH 4.5, 25% w/v Polyethylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97919 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.9185
pseudo-merohedral22-L, -K, -H20.0815
ReflectionResolution: 2.7→40.95 Å / Num. obs: 9099 / % possible obs: 95.55 % / Redundancy: 5.29 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 10.9
Reflection shellResolution: 2.7→2.79 Å / Redundancy: 5.32 % / Rmerge(I) obs: 0.748 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 924 / CC1/2: 0.805 / % possible all: 95.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.95 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU B: 47.161 / SU ML: 0.451 / Cross valid method: THROUGHOUT / ESU R Free: 0.453
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2877 483 5.309 %
Rwork0.2631 8615 -
all0.264 --
obs-9098 93.862 %
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: 117.165 Å2
Baniso -1Baniso -2Baniso -3
1-2.966 Å20 Å22.857 Å2
2---2.26 Å2-0 Å2
3----2.036 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 10 3 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122741
X-RAY DIFFRACTIONr_bond_other_d0.0180.0162626
X-RAY DIFFRACTIONr_ext_dist_refined_b00.143032
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.6393694
X-RAY DIFFRACTIONr_angle_other_deg0.6331.5636131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5055343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.481014
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97310512
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.47910114
X-RAY DIFFRACTIONr_chiral_restr0.0710.2432
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023031
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02481
X-RAY DIFFRACTIONr_nbd_refined0.1880.2545
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2180.22808
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21345
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.21537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.27
X-RAY DIFFRACTIONr_nbd_other0.2570.227
X-RAY DIFFRACTIONr_mcbond_it12.9838.7431381
X-RAY DIFFRACTIONr_mcbond_other12.988.7431381
X-RAY DIFFRACTIONr_mcangle_it18.55913.1111721
X-RAY DIFFRACTIONr_mcangle_other18.55313.1131722
X-RAY DIFFRACTIONr_scbond_it12.9669.4011360
X-RAY DIFFRACTIONr_scbond_other12.9319.4081353
X-RAY DIFFRACTIONr_scangle_it19.04113.8371973
X-RAY DIFFRACTIONr_scangle_other19.06913.8541962
X-RAY DIFFRACTIONr_lrange_it28.921323.76443078
X-RAY DIFFRACTIONr_lrange_other28.921323.75943079
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7670.347330.279652X-RAY DIFFRACTION95.9384
2.767-2.8420.371310.314639X-RAY DIFFRACTION96.6811
2.842-2.9240.351350.331605X-RAY DIFFRACTION96.3855
2.924-3.0140.364290.374579X-RAY DIFFRACTION95.899
3.014-3.1120.455330.348574X-RAY DIFFRACTION95.4403
3.112-3.2210.36360.342547X-RAY DIFFRACTION93.28
3.221-3.3410.407280.334524X-RAY DIFFRACTION94.198
3.341-3.4770.396280.328516X-RAY DIFFRACTION95.6063
3.477-3.630.411210.374497X-RAY DIFFRACTION95.9259
3.63-3.8060.398240.297470X-RAY DIFFRACTION94.4551
3.806-4.010.282300.29432X-RAY DIFFRACTION94.6721
4.01-4.2510.252280.24424X-RAY DIFFRACTION94.3633
4.251-4.5410.26300.251385X-RAY DIFFRACTION93.4685
4.541-4.8990.285220.23354X-RAY DIFFRACTION91.0412
4.899-5.3590.222160.255342X-RAY DIFFRACTION91.0941
5.359-5.9790.322210.24292X-RAY DIFFRACTION90.4624
5.979-6.880.312130.235266X-RAY DIFFRACTION87.1875
6.88-8.3670.123120.21231X-RAY DIFFRACTION90.6716
8.367-11.5930.39230.16189X-RAY DIFFRACTION87.6712
11.593-40.950.178100.27197X-RAY DIFFRACTION78.6765
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.68320.2830.28010.1492-0.59122.84070.05880.20670.3908-0.0751-0.11810.02860.37980.5790.05930.08210.0466-0.03610.1730.00070.378320.0434-1.018315.0201
23.81080.02271.44030.2823-0.75622.8079-0.2334-0.17750.398-0.07240.42250.03060.1858-1.3317-0.18910.0592-0.1319-0.12230.7710.09470.3597-6.6171-0.641517.7878
Refinement TLS groupSelection: ALL

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