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- PDB-6yud: Structure of Csx3/Crn3 from Archaeoglobus fulgidus in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6yud
TitleStructure of Csx3/Crn3 from Archaeoglobus fulgidus in complex with cyclic tetra-adenylate (cA4)
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • Uncharacterized protein AF_1864
KeywordsRNA BINDING PROTEIN / ring nuclease / CRISPcyclo tetra-adenylate
Function / homologyCRISPR-associated protein Csx3 / CRISPR-associated protein (Cas_csx3) / : / RNA / Uncharacterized protein AF_1864
Function and homology information
Biological speciesArchaeoglobus fulgidus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsMcQuarrie, S. / Gloster, T.M. / White, M.F. / Graham, S. / Athukoralage, J.S. / Gruschow, S.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust204821/Z/16/Z United Kingdom
Other governmentBBSRC BB/S000313/1 United Kingdom
Other governmentBBSRC BB/T004789/1 United Kingdom
CitationJournal: Elife / Year: 2020
Title: Tetramerisation of the CRISPR ring nuclease Crn3/Csx3 facilitates cyclic oligoadenylate cleavage.
Authors: Athukoralage, J.S. / McQuarrie, S. / Gruschow, S. / Graham, S. / Gloster, T.M. / White, M.F.
History
DepositionApr 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 13, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_entry_details / pdbx_molecule_features / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _atom_site.auth_seq_id / _database_2.pdbx_DOI ..._atom_site.auth_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_entry_details.compound_details / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _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_ref.db_code / _struct_ref.pdbx_db_accession / _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 / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 2.1Jan 24, 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
A: Uncharacterized protein AF_1864
B: Uncharacterized protein AF_1864
C: Uncharacterized protein AF_1864
D: Uncharacterized protein AF_1864
E: Uncharacterized protein AF_1864
F: Uncharacterized protein AF_1864
G: Uncharacterized protein AF_1864
H: Uncharacterized protein AF_1864
I: Uncharacterized protein AF_1864
J: Uncharacterized protein AF_1864
K: Cyclic tetraadenosine monophosphate (cA4)
M: Cyclic tetraadenosine monophosphate (cA4)
O: Cyclic tetraadenosine monophosphate (cA4)
P: Cyclic tetraadenosine monophosphate (cA4)
Q: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)130,37415
Polymers130,37415
Non-polymers00
Water10,359575
1
A: Uncharacterized protein AF_1864
B: Uncharacterized protein AF_1864
K: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)26,0753
Polymers26,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uncharacterized protein AF_1864
D: Uncharacterized protein AF_1864
O: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)26,0753
Polymers26,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Uncharacterized protein AF_1864
F: Uncharacterized protein AF_1864
P: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)26,0753
Polymers26,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Uncharacterized protein AF_1864
H: Uncharacterized protein AF_1864

M: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)26,0753
Polymers26,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
5
I: Uncharacterized protein AF_1864
J: Uncharacterized protein AF_1864
Q: Cyclic tetraadenosine monophosphate (cA4)


Theoretical massNumber of molelcules
Total (without water)26,0753
Polymers26,0753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.969, 60.364, 107.085
Angle α, β, γ (deg.)90.000, 116.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-260-

HOH

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Components

#1: Protein
Uncharacterized protein AF_1864


Mass: 12401.487 Da / Num. of mol.: 10 / Mutation: H60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1864 / Production host: Escherichia coli (E. coli) / References: UniProt: O28415
#2: RNA chain
Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 5 / 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


Mass: 18.015 Da / Num. of mol.: 575 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 100mM Hepes 25% (v/v) Jeffamine M-600 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.84→53.56 Å / Num. obs: 93596 / % possible obs: 97.1 % / Redundancy: 3.2 % / CC1/2: 0.995 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Net I/σ(I): 11.3 / Num. measured all: 302768 / Scaling rejects: 211
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.892.40.7241283352870.7390.5470.9131.174.5
8.23-53.563.40.029393711600.9760.0190.0354699.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
xia20.5.900-ga3de5862-dials-1.14data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wzi

3wzi


Resolution: 1.84→53.56 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.992 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 4770 5.1 %RANDOM
Rwork0.1924 ---
obs0.1947 88795 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.95 Å2 / Biso mean: 34.154 Å2 / Biso min: 14.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-2.95 Å2
2---0.45 Å20 Å2
3---1.97 Å2
Refinement stepCycle: final / Resolution: 1.84→53.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7586 0 440 577 8603
Biso mean--35.8 43.94 -
Num. residues----998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138317
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177669
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.64811441
X-RAY DIFFRACTIONr_angle_other_deg1.2571.57117651
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3565997
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.4220.619323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.463151216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4571543
X-RAY DIFFRACTIONr_chiral_restr0.0730.21175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021680
LS refinement shellResolution: 1.84→1.887 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 257 -
Rwork0.367 4908 -
obs--72.57 %

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