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- PDB-8pe3: Structure of Csm6' from Streptococcus thermophilus in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8pe3
TitleStructure of Csm6' from Streptococcus thermophilus in complex with cyclic hexa-adenylate (cA6)
Components
  • CRISPR system endoribonuclease Csm6'
  • Cyclic hexaadenosine monophosphate (cA6)
  • RNA
KeywordsRNA BINDING PROTEIN / CARF / HEPN / cA6 / RNAse
Function / homologyCRISPR-associated protein Csm6 / CRISPR-associated protein (Cas_Csm6) / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / RNA binding / RNA / CRISPR system endoribonuclease Csm6'
Function and homology information
Biological speciesStreptococcus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsMcQuarrie, S.J. / Athukoralage, J.S. / McMahon, S.A. / Graham, S. / Ackerman, K. / Bode, B.E. / White, M.F. / Gloster, T.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust204821/Z/16/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T004789/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Activation of Csm6 ribonuclease by cyclic nucleotide binding: in an emergency, twist to open.
Authors: McQuarrie, S. / Athukoralage, J.S. / McMahon, S.A. / Graham, S. / Ackermann, K. / Bode, B.E. / White, M.F. / Gloster, T.M.
History
DepositionJun 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.type
Revision 2.0Oct 25, 2023Group: Polymer sequence / Structure summary / Category: entity / entity_poly
Item: _entity.formula_weight / _entity.pdbx_description / _entity_poly.type
Revision 3.0Nov 1, 2023Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_instance_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_validate_rmsd_angle / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly.type / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_gene_src_gene / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id
Revision 3.1Nov 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR system endoribonuclease Csm6'
B: CRISPR system endoribonuclease Csm6'
C: Cyclic hexaadenosine monophosphate (cA6)
D: RNA
E: RNA


Theoretical massNumber of molelcules
Total (without water)93,9885
Polymers93,9885
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.906, 99.906, 286.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CRISPR system endoribonuclease Csm6' / CRISPR type III-A associated protein Csm6-2


Mass: 45104.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm6' / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A7HFE6, Hydrolases; Acting on ester bonds
#2: RNA chain Cyclic hexaadenosine monophosphate (cA6)


Mass: 1930.277 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA /


Mass: 924.645 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.85 M sodium malonate and 5 % ethanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.96→94.33 Å / Num. obs: 57416 / % possible obs: 95.1 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Net I/σ(I): 14.8
Reflection shellResolution: 1.96→2.2 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.352 / Num. unique obs: 2872 / CC1/2: 0.78 / Rpim(I) all: 0.382 / Rrim(I) all: 1.405 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
STARANISOdata scaling
autoPROCdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→22.34 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2894 5.05 %
Rwork0.1976 --
obs0.1996 57294 54.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→22.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6030 0 264 293 6587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066449
X-RAY DIFFRACTIONf_angle_d0.878782
X-RAY DIFFRACTIONf_dihedral_angle_d10.9521072
X-RAY DIFFRACTIONf_chiral_restr0.0511010
X-RAY DIFFRACTIONf_plane_restr0.0081103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.990.556430.3969X-RAY DIFFRACTION1
1.99-2.030.5168190.3071225X-RAY DIFFRACTION5
2.03-2.060.43190.3448396X-RAY DIFFRACTION8
2.06-2.10.3795240.3524514X-RAY DIFFRACTION11
2.1-2.150.2405280.316663X-RAY DIFFRACTION14
2.15-2.190.299440.3197830X-RAY DIFFRACTION18
2.19-2.240.3738590.3156968X-RAY DIFFRACTION21
2.24-2.30.317490.29871165X-RAY DIFFRACTION25
2.3-2.360.306700.30981438X-RAY DIFFRACTION31
2.36-2.430.3185840.29131708X-RAY DIFFRACTION36
2.43-2.510.35471170.29241987X-RAY DIFFRACTION43
2.51-2.60.32921570.29822624X-RAY DIFFRACTION56
2.6-2.70.31211900.28273636X-RAY DIFFRACTION77
2.7-2.830.2962210.27834381X-RAY DIFFRACTION93
2.83-2.980.28782190.26324752X-RAY DIFFRACTION100
2.98-3.160.3072410.24124758X-RAY DIFFRACTION100
3.16-3.40.25452450.20654766X-RAY DIFFRACTION100
3.41-3.750.22572690.17364769X-RAY DIFFRACTION100
3.75-4.280.19292930.14644790X-RAY DIFFRACTION100
4.29-5.390.17732560.14194878X-RAY DIFFRACTION100
5.39-22.340.20462870.16895083X-RAY DIFFRACTION99

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