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- PDB-6scf: A viral anti-CRISPR subverts type III CRISPR immunity by rapid de... -

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Basic information

Entry
Database: PDB / ID: 6scf
TitleA viral anti-CRISPR subverts type III CRISPR immunity by rapid degradation of cyclic oligoadenylate
Components
  • Uncharacterized protein
  • cyclic oligoadenylate
KeywordsDNA / CRISPR cyclic oligoadenylate DNA anti-CRISPR viral
Function / homologySTIV B116-like / STIV B116-like superfamily / STIV B116-like / Uncharacterised protein PF08960, DUF1874 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / RNA / Uncharacterized protein 114
Function and homology information
Biological speciesSulfolobus islandicus rod-shaped virus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMcMahon, S.A. / Athukoralage, J.S. / Graham, S. / White, M.F. / Gloster, T.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R008035/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S000313/1 United Kingdom
CitationJournal: Nature / Year: 2020
Title: An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity.
Authors: Athukoralage, J.S. / McMahon, S.A. / Zhang, C. / Gruschow, S. / Graham, S. / Krupovic, M. / Whitaker, R.J. / Gloster, T.M. / White, M.F.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Feb 5, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
K: cyclic oligoadenylate
I: cyclic oligoadenylate
L: cyclic oligoadenylate
M: cyclic oligoadenylate


Theoretical massNumber of molelcules
Total (without water)134,74712
Polymers134,74712
Non-polymers00
Water10,665592
1
A: Uncharacterized protein
K: cyclic oligoadenylate

H: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)33,6873
Polymers33,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area5150 Å2
ΔGint-10 kcal/mol
Surface area10340 Å2
MethodPISA
2
B: Uncharacterized protein
G: Uncharacterized protein
I: cyclic oligoadenylate


Theoretical massNumber of molelcules
Total (without water)33,6873
Polymers33,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-10 kcal/mol
Surface area10570 Å2
MethodPISA
3
C: Uncharacterized protein
E: Uncharacterized protein
L: cyclic oligoadenylate


Theoretical massNumber of molelcules
Total (without water)33,6873
Polymers33,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-10 kcal/mol
Surface area10370 Å2
MethodPISA
4
D: Uncharacterized protein
F: Uncharacterized protein
M: cyclic oligoadenylate


Theoretical massNumber of molelcules
Total (without water)33,6873
Polymers33,6873
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-9 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.829, 51.727, 85.611
Angle α, β, γ (deg.)80.220, 89.680, 83.380
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASPASPAA2 - 11426 - 138
21ASNASNASPASPBB2 - 11426 - 138
12ASNASNILEILEAA2 - 11226 - 136
22ASNASNILEILECC2 - 11226 - 136
13ASNASNILEILEAA2 - 11226 - 136
23ASNASNILEILEDD2 - 11226 - 136
14LYSLYSVALVALAA3 - 11327 - 137
24LYSLYSVALVALEE3 - 11327 - 137
15ASNASNVALVALAA2 - 11326 - 137
25ASNASNVALVALFF2 - 11326 - 137
16ASNASNILEILEAA2 - 11226 - 136
26ASNASNILEILEGG2 - 11226 - 136
17ASNASNVALVALAA2 - 11326 - 137
27ASNASNVALVALHH2 - 11326 - 137
18ASNASNILEILEBB2 - 11226 - 136
28ASNASNILEILECC2 - 11226 - 136
19ASNASNILEILEBB2 - 11226 - 136
29ASNASNILEILEDD2 - 11226 - 136
110LYSLYSVALVALBB3 - 11327 - 137
210LYSLYSVALVALEE3 - 11327 - 137
111ASNASNVALVALBB2 - 11326 - 137
211ASNASNVALVALFF2 - 11326 - 137
112ASNASNILEILEBB2 - 11226 - 136
212ASNASNILEILEGG2 - 11226 - 136
113ASNASNVALVALBB2 - 11326 - 137
213ASNASNVALVALHH2 - 11326 - 137
114ASNASNVALVALCC2 - 11326 - 137
214ASNASNVALVALDD2 - 11326 - 137
115LYSLYSILEILECC3 - 11227 - 136
215LYSLYSILEILEEE3 - 11227 - 136
116ASNASNILEILECC2 - 11226 - 136
216ASNASNILEILEFF2 - 11226 - 136
117ASNASNVALVALCC2 - 11326 - 137
217ASNASNVALVALGG2 - 11326 - 137
118ASNASNVALVALCC2 - 11326 - 137
218ASNASNVALVALHH2 - 11326 - 137
119LYSLYSILEILEDD3 - 11227 - 136
219LYSLYSILEILEEE3 - 11227 - 136
120ASNASNILEILEDD2 - 11226 - 136
220ASNASNILEILEFF2 - 11226 - 136
121ASNASNVALVALDD2 - 11326 - 137
221ASNASNVALVALGG2 - 11326 - 137
122ASNASNVALVALDD2 - 11326 - 137
222ASNASNVALVALHH2 - 11326 - 137
123LYSLYSVALVALEE3 - 11327 - 137
223LYSLYSVALVALFF3 - 11327 - 137
124LYSLYSILEILEEE3 - 11227 - 136
224LYSLYSILEILEGG3 - 11227 - 136
125LYSLYSVALVALEE3 - 11327 - 137
225LYSLYSVALVALHH3 - 11327 - 137
126ASNASNILEILEFF2 - 11226 - 136
226ASNASNILEILEGG2 - 11226 - 136
127ASNASNVALVALFF2 - 11326 - 137
227ASNASNVALVALHH2 - 11326 - 137
128ASNASNVALVALGG2 - 11326 - 137
228ASNASNVALVALHH2 - 11326 - 137

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Uncharacterized protein


Mass: 16207.453 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus rod-shaped virus 1
Gene: 114 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8QL27
#2: RNA chain
cyclic oligoadenylate


Mass: 1271.866 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.02 % / Description: large crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40 % MPD, 5 % PEG 8000 and 0.1 M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.55→50.64 Å / Num. obs: 119765 / % possible obs: 98.6 % / Redundancy: 2.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.118 / Net I/σ(I): 12.3
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5590 / CC1/2: 0.79 / % possible all: 92.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2x4i

2x4i


Resolution: 1.55→50.64 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.72 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5883 4.9 %RANDOM
Rwork0.2015 ---
obs0.2039 113882 98.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 349.48 Å2 / Biso mean: 19.601 Å2 / Biso min: 2.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.06 Å2-0.97 Å2
2---0.71 Å20.88 Å2
3---0.75 Å2
Refinement stepCycle: final / Resolution: 1.55→50.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7222 0 352 595 8169
Biso mean--13.26 30.77 -
Num. residues----897
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0197862
X-RAY DIFFRACTIONr_bond_other_d0.0010.027446
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.97510695
X-RAY DIFFRACTIONr_angle_other_deg0.7582.97417380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225924
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.89426.471340
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0651524
X-RAY DIFFRACTIONr_chiral_restr0.0910.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028345
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021379
X-RAY DIFFRACTIONr_rigid_bond_restr4.849315308
X-RAY DIFFRACTIONr_sphericity_free33.8695348
X-RAY DIFFRACTIONr_sphericity_bonded13.591515410
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A35330.08
12B35330.08
21A34130.08
22C34130.08
31A33420.08
32D33420.08
41A32930.11
42E32930.11
51A32960.12
52F32960.12
61A33210.11
62G33210.11
71A32400.11
72H32400.11
81B35680.08
82C35680.08
91B34910.08
92D34910.08
101B34460.1
102E34460.1
111B34570.11
112F34570.11
121B34560.11
122G34560.11
131B33920.1
132H33920.1
141C35450.06
142D35450.06
151C33690.1
152E33690.1
161C33920.11
162F33920.11
171C34700.1
172G34700.1
181C33490.11
182H33490.11
191D34110.09
192E34110.09
201D34230.09
202F34230.09
211D34930.1
212G34930.1
221D33700.1
222H33700.1
231E34130.08
232F34130.08
241E33490.09
242G33490.09
251E32630.1
252H32630.1
261F34150.09
262G34150.09
271F33180.1
272H33180.1
281G33780.08
282H33780.08
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 399 -
Rwork0.309 7906 -
all-8305 -
obs--92.39 %

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