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- PDB-7z56: Crystal Structure of the Ring Nuclease 0455 from Sulfolobus islan... -

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Basic information

Entry
Database: PDB / ID: 7z56
TitleCrystal Structure of the Ring Nuclease 0455 from Sulfolobus islandicus (Sis0455) in its apo form
ComponentsCRISPR-associated protein
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) / CRISPR system ring nuclease SSO2081-like domain-containing protein
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1.2Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Oct 16, 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
AAA: CRISPR-associated protein
BBB: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)47,2582
Polymers47,2582
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-15 kcal/mol
Surface area16840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.423, 51.000, 80.353
Angle α, β, γ (deg.)90.000, 98.696, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR-associated protein


Mass: 23629.191 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1.83 Å3/Da / Density % sol: 32.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% PEG 4000 0.05 M Tricine pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→79.43 Å / Num. obs: 19381 / % possible obs: 85.2 % / Redundancy: 6.3 % / CC1/2: 0.995 / Net I/σ(I): 9.7
Reflection shellResolution: 1.91→2.05 Å / Num. unique obs: 970 / CC1/2: 0.191

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7Z55

7z55


Resolution: 2.27→79.429 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 17.659 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / ESU R: 0.385 / ESU R Free: 0.258
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 776 4.932 %
Rwork0.1815 14957 -
all0.185 --
obs-15733 98.801 %
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: 54.421 Å2
Baniso -1Baniso -2Baniso -3
1-0.316 Å2-0 Å2-0.287 Å2
2---0.496 Å2-0 Å2
3---0.256 Å2
Refinement stepCycle: LAST / Resolution: 2.27→79.429 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 0 30 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132892
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162906
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.6423901
X-RAY DIFFRACTIONr_angle_other_deg1.3731.5866715
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73824.173139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64615572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8071514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023192
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02592
X-RAY DIFFRACTIONr_nbd_refined0.2180.2588
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22842
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21424
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.267
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1780.223
X-RAY DIFFRACTIONr_nbd_other0.2020.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1930.25
X-RAY DIFFRACTIONr_mcbond_it3.1574.3691442
X-RAY DIFFRACTIONr_mcbond_other3.1464.3671441
X-RAY DIFFRACTIONr_mcangle_it4.636.5441799
X-RAY DIFFRACTIONr_mcangle_other4.6296.5481800
X-RAY DIFFRACTIONr_scbond_it4.115.1291450
X-RAY DIFFRACTIONr_scbond_other4.1095.1321451
X-RAY DIFFRACTIONr_scangle_it6.7967.4222102
X-RAY DIFFRACTIONr_scangle_other6.7947.4252103
X-RAY DIFFRACTIONr_lrange_it8.95552.4673131
X-RAY DIFFRACTIONr_lrange_other8.95352.4853130
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
2.27-2.3290.315490.25710740.25911850.8190.84694.76790.238
2.329-2.3930.252530.21210360.21411090.8850.8998.19660.194
2.393-2.4620.298570.20510710.2111400.8570.90298.94740.188
2.462-2.5380.252660.19610070.210780.8950.91299.53620.18
2.538-2.6210.271460.1849710.18710220.8850.92299.51080.175
2.621-2.7130.248340.1969610.19810000.8860.90899.50.181
2.713-2.8150.321530.2099350.2159930.8640.89599.49650.193
2.815-2.930.287510.1948560.1989150.8630.91699.12570.181
2.93-3.060.272520.1898510.1949180.910.92698.3660.182
3.06-3.2090.241480.1768150.1798670.9150.93699.53860.17
3.209-3.3820.261390.1827640.1858060.8990.93899.62780.181
3.382-3.5870.245460.1727320.1767820.8840.94499.48850.178
3.587-3.8340.229280.1757090.1777380.9130.94299.86450.186
3.834-4.140.29300.1686510.1736860.9220.94699.27110.19
4.14-4.5340.2320.1635750.1656250.9570.95897.120.188
4.534-5.0670.207270.1585450.165730.9550.9699.82550.181
5.067-5.8470.262220.1774800.1815050.9220.9599.40590.207
5.847-7.1520.29170.2014210.2044420.9130.94199.0950.235
7.152-10.0730.249180.1573100.1613390.9430.97296.75520.185
10.073-79.4290.23880.2141930.2152010.9760.961000.265
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)
10.76580.05560.79390.38450.03092.20830.08250.00150.02680.0234-0.05390.01350.1242-0.1162-0.02860.0113-0.001-0.00090.1495-0.00270.025618.857-7.9588.33
21.1444-0.0634-0.31530.33380.43863.90590.0296-0.09110.03950.0362-0.0672-0.0026-0.133-0.00060.03760.0265-0.03090.00080.1052-0.01890.005730.0860.94735.616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 179
2X-RAY DIFFRACTION2ALLBBB2 - 184

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