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- PDB-7pq2: Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islan... -

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Basic information

Entry
Database: PDB / ID: 7pq2
TitleCrystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in its apo form
ComponentsCRISPR-associated protein, APE2256 family, CRISPR Ring Nuclease
KeywordsANTIVIRAL PROTEIN / RING NUCLEASE / CRISPR-ASSOCIATED PROTEIN / HELIX-TURN-HELIX / VIRAL RESISTANCE / CARF NUCLEOTIDE-BINDING DOMAIN / CRISPR Ring Nuclease
Function / homologyCRISPR system ring nuclease SSO1393 / CRISPR system ring nuclease SSO1393-like / CRISPR-associated protein (Cas_APE2256) / CRISPR-associated protein, APE2256 family
Function and homology information
Biological speciesSulfolobus islandicus REY15A (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsMolina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF14CC0001 Denmark
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: Structural basis of cyclic oligoadenylate degradation by ancillary Type III CRISPR-Cas ring nucleases.
Authors: Molina, R. / Jensen, A.L.G. / Marchena-Hurtado, J. / Lopez-Mendez, B. / Stella, S. / Montoya, G.
History
DepositionSep 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / entity / struct_keywords
Item: _entity.pdbx_description / _struct_keywords.text
Revision 1.3Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: CRISPR-associated protein, APE2256 family, CRISPR Ring Nuclease
BBB: CRISPR-associated protein, APE2256 family, CRISPR Ring Nuclease


Theoretical massNumber of molelcules
Total (without water)63,3082
Polymers63,3082
Non-polymers00
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-31 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.372, 106.436, 78.443
Angle α, β, γ (deg.)90.000, 102.919, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains AAA BBB)

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Components

#1: Protein CRISPR-associated protein, APE2256 family, CRISPR Ring Nuclease


Mass: 31654.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic)
Gene: SiRe_0811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NH89
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3000, 0.1M CHES pH 9.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.38→61.73 Å / Num. obs: 24724 / % possible obs: 99.9 % / Redundancy: 7 % / CC1/2: 0.99 / Net I/σ(I): 14.1
Reflection shellResolution: 2.38→2.43 Å / Num. unique obs: 1241 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QYF

3qyf


Resolution: 2.38→61.61 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 15.932 / SU ML: 0.182 / Cross valid method: FREE R-VALUE / ESU R: 0.454 / ESU R Free: 0.25
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2226 1176 4.972 %
Rwork0.1634 22478 -
all0.166 --
obs-23654 95.084 %
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: 42.532 Å2
Baniso -1Baniso -2Baniso -3
1-0.032 Å20 Å20.004 Å2
2---0.033 Å20 Å2
3----0.001 Å2
Refinement stepCycle: LAST / Resolution: 2.38→61.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 0 254 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124524
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6336099
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2395545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11623.982226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29815874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6261518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023332
X-RAY DIFFRACTIONr_nbd_refined0.2240.22035
X-RAY DIFFRACTIONr_nbtor_refined0.320.23129
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2249
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1930.229
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1510.212
X-RAY DIFFRACTIONr_mcbond_it2.5443.2982186
X-RAY DIFFRACTIONr_mcangle_it4.0434.9352728
X-RAY DIFFRACTIONr_scbond_it3.763.7462338
X-RAY DIFFRACTIONr_scangle_it5.9165.4093370
X-RAY DIFFRACTIONr_lrange_it8.97361.9118853
X-RAY DIFFRACTIONr_ncsr_local_group_10.140.058348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.4420.311660.2571257X-RAY DIFFRACTION71.9022
2.442-2.5080.331820.2211329X-RAY DIFFRACTION79.9433
2.508-2.5810.244610.2131454X-RAY DIFFRACTION86.8195
2.581-2.660.251680.2251517X-RAY DIFFRACTION93.8425
2.66-2.7480.267860.1931534X-RAY DIFFRACTION99.6923
2.748-2.8440.254950.1791478X-RAY DIFFRACTION100
2.844-2.9510.298810.1771448X-RAY DIFFRACTION100
2.951-3.0710.216670.1661409X-RAY DIFFRACTION99.9323
3.071-3.2080.196650.151344X-RAY DIFFRACTION99.9291
3.208-3.3640.2660.1661278X-RAY DIFFRACTION100
3.364-3.5460.229640.161221X-RAY DIFFRACTION99.9222
3.546-3.760.186540.141162X-RAY DIFFRACTION100
3.76-4.0190.209490.1451096X-RAY DIFFRACTION99.9127
4.019-4.340.191440.1391034X-RAY DIFFRACTION100
4.34-4.7530.192520.132920X-RAY DIFFRACTION99.8972
4.753-5.3110.174500.142842X-RAY DIFFRACTION100
5.311-6.1280.257430.169746X-RAY DIFFRACTION99.8734
6.128-7.4930.293420.2628X-RAY DIFFRACTION100
7.493-10.5460.152290.126500X-RAY DIFFRACTION100
10.546-61.610.204120.161281X-RAY DIFFRACTION97.6667
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)
10.7613-0.19370.32250.0502-0.08140.5164-0.0544-0.0105-0.03170.01220.00180.0038-0.0905-0.12940.05260.01880.0227-0.00170.1005-0.01050.035-31.612-11.37413.179
20.176-0.18210.18980.2759-0.26740.40540.0158-0.00670.03630.00650.0167-0.0030.01070.0052-0.03250.0083-0.00040.00860.0867-0.01110.0353-15.976-19.15327.636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 275
2X-RAY DIFFRACTION2ALLBBB1 - 272

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