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- PDB-7pq6: Crystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulf... -

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Basic information

Entry
Database: PDB / ID: 7pq6
TitleCrystal Structure of the Ring Nuclease 0811 mutant-S12A from Sulfolobus islandicus (Sis0811)
ComponentsCRISPR-associated protein, APE2256 family
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 / : / SSO1393-like, winged-helix domain / CRISPR system ring nuclease SSO1393-like / CRISPR-associated protein (Cas_APE2256) / CRISPR-associated protein, APE2256 family
Function and homology information
Biological speciesSulfolobus islandicus REY15A (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / struct_keywords / struct_ncs_dom_lim
Item: _struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_keywords.text / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
BBB: CRISPR-associated protein, APE2256 family


Theoretical massNumber of molelcules
Total (without water)63,2762
Polymers63,2762
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-31 kcal/mol
Surface area23370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.054, 103.735, 77.678
Angle α, β, γ (deg.)90.000, 102.990, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 1 - 271 / Label seq-ID: 1 - 271

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein CRISPR-associated protein, APE2256 family


Mass: 31638.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus REY15A (archaea) / Gene: SiRe_0811 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: F0NH89
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.1M Bis-Tris propane pH 7.5, 0.2M KSCN

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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: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.67→60.82 Å / Num. obs: 16673 / % possible obs: 98 % / Redundancy: 6.3 % / CC1/2: 0.945 / Net I/σ(I): 6.7
Reflection shellResolution: 2.67→2.714 Å / Num. unique obs: 3165 / CC1/2: 0.494

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PQ2

7pq2


Resolution: 2.67→60.82 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.808 / SU B: 33.283 / SU ML: 0.317 / Cross valid method: FREE R-VALUE / ESU R Free: 0.414
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2795 839 5.171 %
Rwork0.22 15386 -
all0.223 --
obs-16225 95.531 %
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: 38.112 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0 Å2-0.068 Å2
2---0.094 Å2-0 Å2
3---0.321 Å2
Refinement stepCycle: LAST / Resolution: 2.67→60.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4440 0 0 3 4443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134522
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164411
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.6396097
X-RAY DIFFRACTIONr_angle_other_deg1.2561.58510205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365545
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93823.982226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.36615872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.8121518
X-RAY DIFFRACTIONr_chiral_restr0.070.2573
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02971
X-RAY DIFFRACTIONr_nbd_refined0.2050.21005
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.24175
X-RAY DIFFRACTIONr_nbtor_refined0.170.22191
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22334
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.223
X-RAY DIFFRACTIONr_nbd_other0.2830.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1760.27
X-RAY DIFFRACTIONr_mcbond_it1.9543.0942186
X-RAY DIFFRACTIONr_mcbond_other1.9523.092185
X-RAY DIFFRACTIONr_mcangle_it3.4134.6312729
X-RAY DIFFRACTIONr_mcangle_other3.4134.6352730
X-RAY DIFFRACTIONr_scbond_it1.7263.3032334
X-RAY DIFFRACTIONr_scbond_other1.7253.3072335
X-RAY DIFFRACTIONr_scangle_it2.9964.8513367
X-RAY DIFFRACTIONr_scangle_other2.9964.8553368
X-RAY DIFFRACTIONr_lrange_it5.78435.3075107
X-RAY DIFFRACTIONr_lrange_other5.78435.3175108
X-RAY DIFFRACTIONr_ncsr_local_group_10.1550.058125
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.155050.05006
12BBBX-RAY DIFFRACTIONLocal ncs0.155050.05006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.7390.289490.282901X-RAY DIFFRACTION76.1828
2.739-2.8140.304510.2321013X-RAY DIFFRACTION86.7156
2.814-2.8950.303600.2191022X-RAY DIFFRACTION91.6949
2.895-2.9840.309590.2291051X-RAY DIFFRACTION96.6899
2.984-3.0820.295650.2251056X-RAY DIFFRACTION99.0283
3.082-3.190.273590.227981X-RAY DIFFRACTION98.9534
3.19-3.310.294580.207955X-RAY DIFFRACTION97.6856
3.31-3.4450.229350.213974X-RAY DIFFRACTION99.0186
3.445-3.5980.274490.191898X-RAY DIFFRACTION99.0586
3.598-3.7730.225490.185857X-RAY DIFFRACTION99.2333
3.773-3.9770.232510.179825X-RAY DIFFRACTION99.3197
3.977-4.2170.323440.183772X-RAY DIFFRACTION99.0291
4.217-4.5080.26450.191735X-RAY DIFFRACTION98.6094
4.508-4.8670.269440.208662X-RAY DIFFRACTION96.0544
4.867-5.330.273230.232638X-RAY DIFFRACTION99.5482
5.33-5.9550.222250.248581X-RAY DIFFRACTION99.6711
5.955-6.8690.268300.259504X-RAY DIFFRACTION99.2565
6.869-8.3960.314250.269430X-RAY DIFFRACTION99.1285
8.396-11.8010.425120.252333X-RAY DIFFRACTION95.3039
11.801-60.820.36960.338198X-RAY DIFFRACTION96.6825
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)
10.505-0.12640.2790.0393-0.02770.5145-0.0503-0.0964-0.04990.00530.03350.0114-0.0793-0.0810.01670.0240.03610.00830.1509-0.00360.0258-31.5016-11.54313.0866
20.0190.0673-0.08160.6243-0.2661.09730.0278-0.0134-0.00380.04030.0601-0.0058-0.14190.0211-0.08790.04770.0013-0.00220.13720.00670.0166-15.9071-19.048727.3326
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA1 - 275
2X-RAY DIFFRACTION2ALLBBB1 - 272

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