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- PDB-6ov0: Crystal structure of Csm6 in complex with A4>p by soaking A4>p in... -

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Basic information

Entry
Database: PDB / ID: 6ov0
TitleCrystal structure of Csm6 in complex with A4>p by soaking A4>p into Csm6
Components
  • RNA (5'-R(*AP*AP*AP*(A23))-3')
  • Uncharacterized protein
Keywordsimmune system/rna / Type III-A CRISPR-Cas system / Csm6 in complex with cA4 by cocrystallization of Csm6 and cA4 / IMMUNE SYSTEM / immune system-rna complex
Function / homologyCRISPR system endoribonuclease Csx1, HEPN domain / CRISPR system endoribonuclease Csx1 / CRISPR-associated protein DxTHG, conserved site / : / CRISPR system endoribonuclease Csx1, CARF domain / : / RNA / CRISPR system endoribonuclease Csx1 CARF domain-containing protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJia, N. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2019
Title: CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity.
Authors: Jia, N. / Jones, R. / Yang, G. / Ouerfelli, O. / Patel, D.J.
History
DepositionMay 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: RNA (5'-R(*AP*AP*AP*(A23))-3')
F: RNA (5'-R(*AP*AP*AP*(A23))-3')
G: RNA (5'-R(*AP*AP*AP*(A23))-3')
H: RNA (5'-R(*AP*AP*AP*(A23))-3')


Theoretical massNumber of molelcules
Total (without water)204,5168
Polymers204,5168
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.406, 111.456, 113.138
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 49795.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0898 / Variant: NA1 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC3
#2: RNA chain
RNA (5'-R(*AP*AP*AP*(A23))-3')


Mass: 1333.831 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) synthetic construct (others)

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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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 8K, 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 55240 / % possible obs: 98.4 % / Redundancy: 6.9 % / Net I/σ(I): 12.8
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 5482

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O6S

6o6s


Resolution: 2.8→49.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.924 / SU B: 20.303 / SU ML: 0.368 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 5441 9.9 %RANDOM
Rwork0.214 ---
obs0.219 49778 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.48 Å20 Å20.3 Å2
2---2.15 Å20 Å2
3---5.07 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13780 272 0 0 14052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01314390
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713660
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.68219540
X-RAY DIFFRACTIONr_angle_other_deg1.0621.59231608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70551726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.12820.981734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.863152506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415116
X-RAY DIFFRACTIONr_chiral_restr0.0710.21864
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023110
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0348.3826916
X-RAY DIFFRACTIONr_mcbond_other2.0348.3826915
X-RAY DIFFRACTIONr_mcangle_it3.55512.5728638
X-RAY DIFFRACTIONr_mcangle_other3.55512.5738639
X-RAY DIFFRACTIONr_scbond_it1.9028.877474
X-RAY DIFFRACTIONr_scbond_other1.9028.8697472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.41213.20510902
X-RAY DIFFRACTIONr_long_range_B_refined6.11995.55515397
X-RAY DIFFRACTIONr_long_range_B_other6.11995.55415398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 398 -
Rwork0.35 3611 -
obs--97.35 %

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