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- PDB-7bdv: Structure of Can2 from Sulfobacillus thermosulfidooxidans in comp... -

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Basic information

Entry
Database: PDB / ID: 7bdv
TitleStructure of Can2 from Sulfobacillus thermosulfidooxidans in complex with cyclic tetra-adenylate (cA4)
Components
  • Can2
  • Cyclic tetraadenosine monophosphate (cA4)
KeywordsDNA BINDING PROTEIN / CRISPR / cyclic tetra-adenylate / CARF domains / nuclease
Function / homologyProtein of unknown function DUF1887 / Domain of unknown function (DUF1887) / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / : / RNA / Can2
Function and homology information
Biological speciesSulfobacillus thermosulfidooxidans (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsMcQuarrie, S. / McMahon, S.A. / Gloster, T.M. / White, M.F. / Graham, S. / Zhu, W. / Gruschow, S.
Funding support United Kingdom, China, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004789/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S000313/1 United Kingdom
Wellcome Trust204821/Z/16/Z United Kingdom
Chinese Academy of Sciences201703780015 China
CitationJournal: Nucleic Acids Res. / Year: 2021
Title: The CRISPR ancillary effector Can2 is a dual-specificity nuclease potentiating type III CRISPR defence.
Authors: Zhu, W. / McQuarrie, S. / Gruschow, S. / McMahon, S.A. / Graham, S. / Gloster, T.M. / White, M.F.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Dec 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_caveat / entity / pdbx_entry_details / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_validate_chiral / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_caveat.text / _entity.pdbx_description / _pdbx_entry_details.compound_details / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id / _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 / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Can2
B: Can2
C: Can2
D: Can2
F: Cyclic tetraadenosine monophosphate (cA4)
H: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)172,7036
Polymers172,7036
Non-polymers00
Water4,900272
1
A: Can2
B: Can2
F: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)86,3513
Polymers86,3513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-9 kcal/mol
Surface area29240 Å2
MethodPISA
2
C: Can2
D: Can2
H: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)86,3513
Polymers86,3513
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-15 kcal/mol
Surface area28350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.860, 85.970, 237.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

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
11HISHISALAALAAA11 - 36611 - 366
21HISHISALAALABB11 - 36611 - 366
12ASPASPASNASNAA12 - 36512 - 365
22ASPASPASNASNCC12 - 36512 - 365
13ARGARGALAALAAA3 - 3663 - 366
23ARGARGALAALADD3 - 3663 - 366
14ASPASPALAALABB12 - 36612 - 366
24ASPASPALAALACC12 - 36612 - 366
15HISHISALAALABB11 - 36611 - 366
25HISHISALAALADD11 - 36611 - 366
16ASPASPALAALACC12 - 36612 - 366
26ASPASPALAALADD12 - 36612 - 366

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Can2


Mass: 42539.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfobacillus thermosulfidooxidans (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A8I3AZU2
#2: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: AntiviralAntiviral drug / Mass: 1271.866 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage.
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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 0.2 M Ammonium nitrate pH 6.3 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→51.37 Å / Num. obs: 102945 / % possible obs: 100 % / Redundancy: 35.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.033 / Rrim(I) all: 0.19 / Net I/σ(I): 16
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 39 % / Rmerge(I) obs: 2.918 / Num. unique obs: 5103 / CC1/2: 0.548 / Rpim(I) all: 0.471 / Rrim(I) all: 2.956 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
CRANKphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.02→51.37 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.36 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.224 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2901 5122 5 %RANDOM
Rwork0.2408 ---
obs0.2433 97728 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.33 Å2 / Biso mean: 47.216 Å2 / Biso min: 23.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.07 Å2
Refinement stepCycle: final / Resolution: 2.02→51.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10522 0 176 273 10971
Biso mean--37.74 49.64 -
Num. residues----1379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179941
X-RAY DIFFRACTIONr_angle_refined_deg1.5341.64715003
X-RAY DIFFRACTIONr_angle_other_deg1.2511.57122661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.451371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17322.495509
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.142151589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6481553
X-RAY DIFFRACTIONr_chiral_restr0.0730.21509
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212609
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022657
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95560.1
12B95560.1
21A98300.1
22C98300.1
31A97880.1
32D97880.1
41B93700.1
42C93700.1
51B92930.09
52D92930.09
61C94520.1
62D94520.1
LS refinement shellResolution: 2.02→2.072 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 363 -
Rwork0.304 7137 -
all-7500 -
obs--99.99 %

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