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- PDB-8b0r: Structure of the CalpL/cA4 complex -

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Basic information

Entry
Database: PDB / ID: 8b0r
TitleStructure of the CalpL/cA4 complex
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • SMODS-associated and fused to various effectors domain-containing protein
KeywordsHYDROLASE / Protease / CRISPR type III / cOA / cA4 / peptide binding protein
Function / homologySMODS-associated and fused to various effectors / SMODS-associated and fused to various effectors sensor domain / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / membrane / : / TRIETHYLENE GLYCOL / RNA / SMODS-associated and fused to various effectors domain-containing protein
Function and homology information
Biological speciesSulfurihydrogenibium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSchneberger, N. / Hagelueken, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)HA 6805/6-1 Germany
CitationJournal: Nature / Year: 2023
Title: Antiviral signalling by a cyclic nucleotide activated CRISPR protease.
Authors: Rouillon, C. / Schneberger, N. / Chi, H. / Blumenstock, K. / Da Vela, S. / Ackermann, K. / Moecking, J. / Peter, M.F. / Boenigk, W. / Seifert, R. / Bode, B.E. / Schmid-Burgk, J.L. / Svergun, ...Authors: Rouillon, C. / Schneberger, N. / Chi, H. / Blumenstock, K. / Da Vela, S. / Ackermann, K. / Moecking, J. / Peter, M.F. / Boenigk, W. / Seifert, R. / Bode, B.E. / Schmid-Burgk, J.L. / Svergun, D. / Geyer, M. / White, M.F. / Hagelueken, G.
History
DepositionSep 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 2.0Jun 28, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_validate_close_contact / struct_ref_seq
Item: _atom_site.auth_seq_id / _pdbx_entry_details.compound_details ..._atom_site.auth_seq_id / _pdbx_entry_details.compound_details / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 2.1Jul 12, 2023Group: Structure summary / Category: pdbx_entry_details / pdbx_molecule_features
Item: _pdbx_entry_details.compound_details / _pdbx_molecule_features.class ..._pdbx_entry_details.compound_details / _pdbx_molecule_features.class / _pdbx_molecule_features.details / _pdbx_molecule_features.name
Revision 3.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Polymer sequence / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / entity / entity_poly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_validate_close_contact / struct_ref_seq
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_seq_id / _atom_site.pdbx_formal_charge / _entity.pdbx_description / _entity_poly.pdbx_strand_id / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_strand_id
Revision 3.1Sep 20, 2023Group: Structure summary / Category: entity / Item: _entity.pdbx_description
Revision 4.0Dec 13, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / pdbx_poly_seq_scheme / pdbx_validate_close_contact / struct_ref_seq
Item: _atom_site.auth_seq_id / _entity.pdbx_description ..._atom_site.auth_seq_id / _entity.pdbx_description / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
Revision 4.1Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMODS-associated and fused to various effectors domain-containing protein
B: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8076
Polymers59,3692
Non-polymers4384
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-37 kcal/mol
Surface area22480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.487, 69.487, 256.288
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

#1: Protein SMODS-associated and fused to various effectors domain-containing protein / SAVED domain-containing protein


Mass: 58096.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfurihydrogenibium (bacteria) / Strain: YO3AOP1 / Gene: SYO3AOP1_0656 / Production host: Escherichia coli (E. coli) / References: UniProt: B2V8L9
#2: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / 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.) Sulfurihydrogenibium (bacteria) / References: BIRD: PRD_002431
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. ...Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. 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 interestN

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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: 3.02 Å3/Da / Density % sol: 59.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-Cl pH 8.0, 38.8 % PEG 400, 0.29 M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.2→54.47 Å / Num. obs: 37616 / % possible obs: 99.98 % / Redundancy: 2 % / Biso Wilson estimate: 36.85 Å2 / CC1/2: 0.999 / CC star: 1 / Rrim(I) all: 0.049 / Net I/σ(I): 8.37
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 3685 / CC1/2: 0.823 / CC star: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.20_4444refinement
PHENIX1.20_4444refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QDA

7qda


Resolution: 2.2→54.47 Å / SU ML: 0.277 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7319
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2671 1993 5.3 %
Rwork0.2361 35622 -
obs0.2378 37615 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.71 Å2
Refinement stepCycle: LAST / Resolution: 2.2→54.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 88 25 165 4356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00164295
X-RAY DIFFRACTIONf_angle_d0.42325813
X-RAY DIFFRACTIONf_chiral_restr0.0414662
X-RAY DIFFRACTIONf_plane_restr0.0032718
X-RAY DIFFRACTIONf_dihedral_angle_d8.7476582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.3221430.27892513X-RAY DIFFRACTION100
2.26-2.320.30881430.26692507X-RAY DIFFRACTION100
2.32-2.380.30951370.28772483X-RAY DIFFRACTION100
2.38-2.460.33451400.26852496X-RAY DIFFRACTION100
2.46-2.550.33891440.2772499X-RAY DIFFRACTION100
2.55-2.650.3131450.27722509X-RAY DIFFRACTION100
2.65-2.770.31611350.28432502X-RAY DIFFRACTION99.96
2.77-2.920.29241400.26842546X-RAY DIFFRACTION100
2.92-3.10.29531370.27722502X-RAY DIFFRACTION100
3.1-3.340.32111460.25752562X-RAY DIFFRACTION100
3.34-3.680.26821380.23032560X-RAY DIFFRACTION100
3.68-4.210.24051430.20732546X-RAY DIFFRACTION100
4.21-5.30.22221430.19432632X-RAY DIFFRACTION100
5.3-54.470.21431590.20762765X-RAY DIFFRACTION99.93

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