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- PDB-6o6z: Crystal structure of Csm6 H381A in complex with cA4 by cocrystall... -

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Basic information

Entry
Database: PDB / ID: 6o6z
TitleCrystal structure of Csm6 H381A in complex with cA4 by cocrystallization of cA4 and Csm6
ComponentsCsm6
KeywordsIMMUNE SYSTEM / Type III-A CRISPR-Cas system / Csm6
Function / homologyCRISPR system endoribonuclease Csx1 / CRISPR-associated protein DxTHG, conserved site / CRISPR system endoribonuclease Csx1-like / CRISPR system endoribonuclease Csx1, HEPN domain / : / Chem-LQJ / CRISPR system endoribonuclease Csx1-like domain-containing protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 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: Csm6
B: Csm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7734
Polymers99,4562
Non-polymers1,3172
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5410 Å2
ΔGint-32 kcal/mol
Surface area34680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.292, 115.940, 159.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Csm6


Mass: 49728.047 Da / Num. of mol.: 2 / Mutation: H381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0898 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC3
#2: Chemical ChemComp-LQJ / 3'-O-[(R)-{[(2S,3aS,4S,6S,6aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLQJ is a result of cA4 cleavage occurred during crystallization

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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: 2.52 Å3/Da / Density % sol: 51.23 %
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-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59191 / % possible obs: 99.4 % / Redundancy: 10.9 % / Rpim(I) all: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 5719

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O6Z

Resolution: 2.1→48.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.255 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.169 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22155 2981 5 %RANDOM
Rwork0.19247 ---
obs0.19394 56115 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.976 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2--2.21 Å20 Å2
3----2.81 Å2
Refinement stepCycle: 1 / Resolution: 2.1→48.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6860 0 88 150 7098
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137107
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176808
X-RAY DIFFRACTIONr_angle_refined_deg1.7281.679635
X-RAY DIFFRACTIONr_angle_other_deg1.3441.5915744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3285857
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25120.986365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.944151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7111558
X-RAY DIFFRACTIONr_chiral_restr0.0830.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027773
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021545
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_it3.6323.943440
X-RAY DIFFRACTIONr_mcbond_other3.6243.9383439
X-RAY DIFFRACTIONr_mcangle_it5.1235.8924293
X-RAY DIFFRACTIONr_mcangle_other5.1235.8944294
X-RAY DIFFRACTIONr_scbond_it5.0414.6383667
X-RAY DIFFRACTIONr_scbond_other5.044.6373668
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6236.6825343
X-RAY DIFFRACTIONr_long_range_B_refined9.59345.797752
X-RAY DIFFRACTIONr_long_range_B_other9.59745.7667740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 222 -
Rwork0.275 3936 -
obs--96.23 %

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