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- PDB-8jh1: Crystal Structure of the Csm6 Y161A mutant from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 8jh1
TitleCrystal Structure of the Csm6 Y161A mutant from Thermus thermophilus HB8 in complex with cyclic-tetraadenylate (cA4)
Components
  • CRISPR system endoribonuclease Csm6
  • RNA (5'-R(P*AP*AP*AP*A)-3')
KeywordsHYDROLASE / Thermus thermophilus HB8 / Csm6 / Endoribonuclease / cyclic-tetraadenylate (cA4)
Function / homologyCsm6 HEPN domain / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA / CRISPR system endoribonuclease Csm6
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsLin, Z. / Du, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Embo J. / Year: 2024
Title: Molecular mechanism of allosteric activation of the CRISPR ribonuclease Csm6 by cyclic tetra-adenylate.
Authors: Du, L. / Zhu, Q. / Lin, Z.
History
DepositionMay 22, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR system endoribonuclease Csm6
B: CRISPR system endoribonuclease Csm6
C: RNA (5'-R(P*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)103,1993
Polymers103,1993
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9970 Å2
ΔGint-40 kcal/mol
Surface area37200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.240, 116.240, 156.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CRISPR system endoribonuclease Csm6 / CRISPR type III-A associated protein Csm6 / TtCsm6


Mass: 50963.664 Da / Num. of mol.: 2 / Mutation: Y161A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Gene: csm6, TTHB152 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta
References: UniProt: Q53W17, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*AP*AP*A)-3')


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.: 34 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Lithium sulfate, 0.1 M Phosphate-citrate pH 4.2, 20% Polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.89→38.85 Å / Num. obs: 24694 / % possible obs: 99.88 % / Redundancy: 25.4 % / CC1/2: 0.999 / Net I/σ(I): 18
Reflection shellResolution: 2.89→2.97 Å / Num. unique obs: 2412 / CC1/2: 0.792

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.89→29.81 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 1999 8.1 %
Rwork0.1965 --
obs0.2011 24672 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.89→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7165 88 0 34 7287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.241
X-RAY DIFFRACTIONf_dihedral_angle_d9.3471075
X-RAY DIFFRACTIONf_chiral_restr0.0611120
X-RAY DIFFRACTIONf_plane_restr0.0121305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-2.960.4221390.30531575X-RAY DIFFRACTION100
2.96-3.040.33291410.27381597X-RAY DIFFRACTION100
3.04-3.130.33481400.26131595X-RAY DIFFRACTION100
3.13-3.230.30341400.23511587X-RAY DIFFRACTION100
3.23-3.350.32171380.23481575X-RAY DIFFRACTION100
3.35-3.480.32511420.24451609X-RAY DIFFRACTION100
3.48-3.640.31711420.21681609X-RAY DIFFRACTION100
3.64-3.830.29241410.21181591X-RAY DIFFRACTION100
3.83-4.070.22731410.18771614X-RAY DIFFRACTION100
4.07-4.380.22071440.17681620X-RAY DIFFRACTION100
4.38-4.820.23791440.17231623X-RAY DIFFRACTION100
4.82-5.520.27041450.18121654X-RAY DIFFRACTION100
5.52-6.940.25231460.19761658X-RAY DIFFRACTION100
6.94-29.810.15791560.15181766X-RAY DIFFRACTION100

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