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- PDB-6o71: Crystal structure of Csm6 in complex with cdA4 by soaking cdA4 in... -

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Basic information

Entry
Database: PDB / ID: 6o71
TitleCrystal structure of Csm6 in complex with cdA4 by soaking cdA4 into Csm6
Components
  • Csm6
  • Cyclic DNA cdA4
Keywordsimmune system/dna / Type III-A CRISPR-Cas system / Csm6 in complex with cdA4 / IMMUNE SYSTEM / immune system-dna complex
Function / homologyCRISPR system endoribonuclease Csx1 / CRISPR-associated protein DxTHG, conserved site / : / CRISPR system endoribonuclease Csx1, CARF domain / : / DNA / 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: 2.55 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
DepositionMar 7, 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 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Csm6
B: Csm6
C: Cyclic DNA cdA4
D: Cyclic DNA cdA4


Theoretical massNumber of molelcules
Total (without water)102,0064
Polymers102,0064
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-11 kcal/mol
Surface area35060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.283, 164.471, 111.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Csm6


Mass: 49795.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_0898 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC3
#2: DNA chain Cyclic DNA cdA4 / DNA (5'-D(P*AP*AP*AP*A)-3')


Mass: 1207.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
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: Feb 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 32217 / % possible obs: 99.8 % / Redundancy: 12.6 % / Net I/σ(I): 11
Reflection shellResolution: 2.55→2.64 Å / Num. unique obs: 3056

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→48.57 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 16.507 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.364 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27346 3160 10.1 %RANDOM
Rwork0.22443 ---
obs0.22942 28036 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.317 Å2
Baniso -1Baniso -2Baniso -3
1-4.89 Å20 Å20 Å2
2---4.45 Å20 Å2
3----0.44 Å2
Refinement stepCycle: 1 / Resolution: 2.55→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 168 0 7058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0137233
X-RAY DIFFRACTIONr_bond_other_d0.0030.0176872
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.699825
X-RAY DIFFRACTIONr_angle_other_deg1.1321.60415898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.73920.981367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.955151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1381558
X-RAY DIFFRACTIONr_chiral_restr0.0440.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027871
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021565
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_it1.4466.9263458
X-RAY DIFFRACTIONr_mcbond_other1.4466.9253457
X-RAY DIFFRACTIONr_mcangle_it2.57510.3864319
X-RAY DIFFRACTIONr_mcangle_other2.57510.3874320
X-RAY DIFFRACTIONr_scbond_it1.2757.3883775
X-RAY DIFFRACTIONr_scbond_other1.2757.3853773
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.30311.025506
X-RAY DIFFRACTIONr_long_range_B_refined4.80279.567723
X-RAY DIFFRACTIONr_long_range_B_other4.80179.5617724
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 218 -
Rwork0.338 1820 -
obs--89.58 %

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