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- PDB-6sce: Structure of a Type III CRISPR defence DNA nuclease activated by ... -

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Basic information

Entry
Database: PDB / ID: 6sce
TitleStructure of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate
Components
  • Uncharacterized protein
  • cyclic oligoadenylate
KeywordsDNA / CRISPR CARF DNA Nuclease cyclic oligoadenylate Thermus thermophilus
Function / homologyRestriction endonuclease type II-like / RNA / CRISPR-associated protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.83 Å
AuthorsMcMahon, S.A. / Zhu, W. / Graham, S. / White, M.F. / Gloster, T.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/R008035/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/S000313/1 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Structure and mechanism of a Type III CRISPR defence DNA nuclease activated by cyclic oligoadenylate.
Authors: McMahon, S.A. / Zhu, W. / Graham, S. / Rambo, R. / White, M.F. / Gloster, T.M.
History
DepositionJul 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: cyclic oligoadenylate


Theoretical massNumber of molelcules
Total (without water)73,5272
Polymers73,5272
Non-polymers00
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-3 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.370, 84.520, 123.100
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 Uncharacterized protein


Mass: 72254.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: TTHB155 / Variant: HB8 / ATCC 27634 / DSM 579 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W14
#2: RNA chain cyclic oligoadenylate


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.2 M sodium citrate, 0.1 M bis-Tris propane, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.82→59.7 Å / Num. obs: 78941 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.43 / Mean I/σ(I) obs: 2 / Num. unique obs: 4460 / CC1/2: 0.755 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
xia2data reduction
xia2data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.83→59.7 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.477 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20944 3921 5 %RANDOM
Rwork0.1765 ---
obs0.17813 74943 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.802 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2---1.14 Å20 Å2
3---2.24 Å2
Refinement stepCycle: LAST / Resolution: 1.83→59.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4832 0 88 412 5332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195145
X-RAY DIFFRACTIONr_bond_other_d0.0010.024794
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9737017
X-RAY DIFFRACTIONr_angle_other_deg0.7862.9911027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7375628
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82721.325234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31415767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0441561
X-RAY DIFFRACTIONr_chiral_restr0.0880.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
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_it2.4583.9992473
X-RAY DIFFRACTIONr_mcbond_other2.4573.9972472
X-RAY DIFFRACTIONr_mcangle_it3.4615.9743090
X-RAY DIFFRACTIONr_mcangle_other3.465.9753091
X-RAY DIFFRACTIONr_scbond_it3.034.3422672
X-RAY DIFFRACTIONr_scbond_other3.034.3422673
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.736.3513920
X-RAY DIFFRACTIONr_long_range_B_refined6.71146.6895901
X-RAY DIFFRACTIONr_long_range_B_other6.71146.6865902
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.825→1.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 299 -
Rwork0.279 5482 -
obs--100 %

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