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- PDB-8jbb: Crystal Structure of the Csm6 from Thermus thermophilus HB8 in co... -

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Basic information

Entry
Database: PDB / ID: 8jbb
TitleCrystal Structure of the Csm6 from Thermus thermophilus HB8 in complex with A2>p
Components
  • CRISPR system endoribonuclease Csm6
  • RNA (5'-R(*AP*(A23))-3')
KeywordsHYDROLASE / Thermus thermophilus HB8 / Csm6 / Endoribonuclease / A2>p
Function / homology: / Csm6 HEPN domain / Csm6 6H domain / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA / CRISPR system endoribonuclease Csm6
Function and homology information
Biological speciesThermus thermophilus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 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 8, 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

Downloads & links

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Assembly

Deposited unit
A: CRISPR system endoribonuclease Csm6
B: CRISPR system endoribonuclease Csm6
C: RNA (5'-R(*AP*(A23))-3')
D: RNA (5'-R(*AP*(A23))-3')


Theoretical massNumber of molelcules
Total (without water)103,7254
Polymers103,7254
Non-polymers00
Water9,728540
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.240, 75.120, 103.690
Angle α, β, γ (deg.)90.000, 95.950, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 51186.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8) (bacteria)
Gene: csm6, TTHB152 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: Q53W17, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(*AP*(A23))-3')


Mass: 675.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.81→60.72 Å / Num. obs: 80762 / % possible obs: 99.54 % / Redundancy: 6.1 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.9
Reflection shellResolution: 1.81→1.86 Å / Num. unique obs: 8016 / CC1/2: 0.447 / % possible all: 99.43

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
HKL-20001.20.1_4487data scaling
MOLREPphasing
Cootmodel building
PHENIXmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→29.68 Å / SU ML: 0.2242 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9055
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2309 3872 2.49 %
Rwork0.1966 151821 -
obs0.1974 80743 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.42 Å2
Refinement stepCycle: LAST / Resolution: 1.81→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7181 88 0 540 7809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787428
X-RAY DIFFRACTIONf_angle_d1.023610088
X-RAY DIFFRACTIONf_chiral_restr0.05731120
X-RAY DIFFRACTIONf_plane_restr0.01171305
X-RAY DIFFRACTIONf_dihedral_angle_d6.4211058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.81-1.830.32021350.32325303X-RAY DIFFRACTION95.79
1.83-1.860.33751370.30125392X-RAY DIFFRACTION97.24
1.86-1.880.28361400.30045483X-RAY DIFFRACTION97.69
1.88-1.910.28741360.28415300X-RAY DIFFRACTION97.28
1.91-1.930.30551370.2895419X-RAY DIFFRACTION97.66
1.93-1.960.3181390.27355470X-RAY DIFFRACTION98.37
1.96-1.990.31491370.26585469X-RAY DIFFRACTION98.71
1.99-2.020.30421450.25145550X-RAY DIFFRACTION98.63
2.02-2.060.25761390.2365401X-RAY DIFFRACTION98.44
2.06-2.10.20961400.22095522X-RAY DIFFRACTION98.81
2.1-2.140.27651410.21945458X-RAY DIFFRACTION98.75
2.14-2.180.28151370.21345403X-RAY DIFFRACTION98.49
2.18-2.230.25091400.21225516X-RAY DIFFRACTION98.4
2.23-2.280.25521410.20085454X-RAY DIFFRACTION98.42
2.28-2.340.25871380.21155493X-RAY DIFFRACTION98.58
2.34-2.40.23241420.20245429X-RAY DIFFRACTION98.38
2.4-2.470.23521360.20765486X-RAY DIFFRACTION98.56
2.47-2.550.25461410.19425443X-RAY DIFFRACTION98.47
2.55-2.640.28021400.20845462X-RAY DIFFRACTION97.92
2.64-2.750.26151350.20385393X-RAY DIFFRACTION97.96
2.75-2.870.22451390.21655449X-RAY DIFFRACTION97.93
2.87-3.020.23581410.20015446X-RAY DIFFRACTION97.64
3.02-3.210.2241410.19915365X-RAY DIFFRACTION97.28
3.21-3.460.21991360.18455387X-RAY DIFFRACTION96.66
3.46-3.810.20441360.17935329X-RAY DIFFRACTION96.18
3.81-4.360.19291340.15935326X-RAY DIFFRACTION95.81
4.36-5.480.20651320.17045330X-RAY DIFFRACTION96.4
5.49-29.680.19461370.16715343X-RAY DIFFRACTION96.09

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