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- PDB-7z55: Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islan... -

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Basic information

Entry
Database: PDB / ID: 7z55
TitleCrystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in complex with its substrate
Components
  • CRISPR-associated protein
  • Cyclic RNA cA4
KeywordsANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease
Function / homologyCRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / ACETATE ION / PHOSPHATE ION / RNA / CRISPR system ring nuclease SSO2081-like domain-containing protein
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.664 Å
AuthorsMolina, R. / Martin-Garcia, R. / Lopez-Mendez, B. / Jensen, A.L.G. / Marchena-Hurtado, J. / Stella, S. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases.
Authors: Molina, R. / Garcia-Martin, R. / Lopez-Mendez, B. / Jensen, A.L.G. / Ciges-Tomas, J.R. / Marchena-Hurtado, J. / Stella, S. / Montoya, G.
History
DepositionMar 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Structure summary / Category: chem_comp_atom / chem_comp_bond / struct_keywords / Item: _struct_keywords.text
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
AAA: CRISPR-associated protein
BBB: CRISPR-associated protein
CCC: Cyclic RNA cA4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0595
Polymers48,9053
Non-polymers1542
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-21 kcal/mol
Surface area16780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.975, 79.531, 95.740
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated protein


Mass: 23816.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Gene: SiRe_0455 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NGX6
#2: RNA chain Cyclic RNA cA4


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.78 Å3/Da / Density % sol: 30.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 41% PEG 400 0.1M sodium acetate pH 4.5 0.1M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.54→61.24 Å / Num. obs: 37215 / % possible obs: 84.2 % / Redundancy: 24.4 % / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 1.54→1.65 Å / Num. unique obs: 1746 / CC1/2: 0.488

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.664→47.916 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.307 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2518 1938 4.991 %
Rwork0.2086 36894 -
all0.211 --
obs-36894 98.859 %
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: 37.293 Å2
Baniso -1Baniso -2Baniso -3
1--0.052 Å20 Å2-0 Å2
2--0.222 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.664→47.916 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 88 9 36 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0133160
X-RAY DIFFRACTIONr_bond_other_d0.0030.0163080
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.6494283
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5857118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3855377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10524.342152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5315579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023451
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02658
X-RAY DIFFRACTIONr_nbd_refined0.2240.2655
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.23057
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21548
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21664
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.251
X-RAY DIFFRACTIONr_nbd_other0.290.2159
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.212
X-RAY DIFFRACTIONr_mcbond_it3.1793.4151512
X-RAY DIFFRACTIONr_mcbond_other3.1553.4131510
X-RAY DIFFRACTIONr_mcangle_it4.3775.1231887
X-RAY DIFFRACTIONr_mcangle_other4.3775.1241888
X-RAY DIFFRACTIONr_scbond_it3.9873.9411648
X-RAY DIFFRACTIONr_scbond_other3.9863.941649
X-RAY DIFFRACTIONr_scangle_it5.7755.7162396
X-RAY DIFFRACTIONr_scangle_other5.7745.7162397
X-RAY DIFFRACTIONr_lrange_it7.33741.1913480
X-RAY DIFFRACTIONr_lrange_other7.33841.1943481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.664-1.7070.1071390.0852649X-RAY DIFFRACTION97.5849
1.707-1.7540.1081380.0922627X-RAY DIFFRACTION99.8916
1.754-1.8050.1391370.1022607X-RAY DIFFRACTION99.8181
1.805-1.860.1391310.1232475X-RAY DIFFRACTION99.8467
1.86-1.9210.3361240.2962372X-RAY DIFFRACTION97.844
1.921-1.9890.2421200.2072301X-RAY DIFFRACTION97.1119
1.989-2.0640.2561170.1982212X-RAY DIFFRACTION97.652
2.064-2.1480.2431160.2042195X-RAY DIFFRACTION99.4406
2.148-2.2430.2951070.2392067X-RAY DIFFRACTION98.9982
2.243-2.3530.3121070.2212012X-RAY DIFFRACTION98.6499
2.353-2.480.2361000.1921908X-RAY DIFFRACTION99.8012
2.48-2.630.247950.2271814X-RAY DIFFRACTION99.5308
2.63-2.8110.308890.2381708X-RAY DIFFRACTION98.5738
2.811-3.0360.284830.231584X-RAY DIFFRACTION98.5225
3.036-3.3250.297790.221492X-RAY DIFFRACTION100
3.325-3.7160.297710.2131348X-RAY DIFFRACTION99.8593
3.716-4.2880.223620.1941203X-RAY DIFFRACTION98.6739
4.288-5.2450.221540.1851013X-RAY DIFFRACTION98.1601
5.245-7.3910.205430.229808X-RAY DIFFRACTION98.1546
7.391-47.9160.259260.228499X-RAY DIFFRACTION99.8099
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)
10.0445-0.02560.04480.03010.00350.10490.00010.0048-0.00230.0025-0.00480.00530.0037-0.00090.00470.0263-0.00080.00270.00140.00010.041626.858-1.42214.277
20.0479-0.01170.05460.04670.0190.0973-0.0018-0.00770.0030.00230.0026-0.00940.0061-0.0051-0.00080.0275-0.00040.00050.00240.0020.039440.825-1.15935.664
30.8723-0.097-0.12620.01090.01430.0192-0.0031-0.0095-0.01780.0020.00060.00170.00650.00010.00250.0406-0.0057-0.00070.00740.00390.036133.896-5.78324.855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 189
2X-RAY DIFFRACTION2ALLBBB2 - 190
3X-RAY DIFFRACTION3ALLCCC1 - 4

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