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- PDB-8jbc: Crystal Structure of the Csm6 K137A mutant from Thermus thermophi... -

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Basic information

Entry
Database: PDB / ID: 8jbc
TitleCrystal Structure of the Csm6 K137A mutant from Thermus thermophilus HB8 in its apo form
ComponentsCRISPR system endoribonuclease Csm6
KeywordsHYDROLASE / Thermus thermophilus HB8 / Csm6 / Endoribonuclease / K137A
Function / homology: / Csm6 HEPN domain / Csm6 6H domain / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / NICKEL (II) ION / CRISPR system endoribonuclease Csm6
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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

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Assembly

Deposited unit
A: CRISPR system endoribonuclease Csm6
B: CRISPR system endoribonuclease Csm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1724
Polymers103,0552
Non-polymers1172
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-59 kcal/mol
Surface area40650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.890, 205.570, 59.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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


Mass: 51527.297 Da / Num. of mol.: 2 / Mutation: K137A
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: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.01 M Magnesium chloride hexahydrate, 0.1M HEPES sodium pH 7.0, 15% 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: 2.41→68.52 Å / Num. obs: 45579 / % possible obs: 99.87 % / Redundancy: 12.9 % / Biso Wilson estimate: 62.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 15
Reflection shellResolution: 2.41→2.47 Å / Num. unique obs: 4483 / CC1/2: 0.676 / % possible all: 99.93

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
HKL-20001.20.1_4487data scaling
MOLREPphasing
PHENIXmodel building
Cootmodel building
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→29.64 Å / SU ML: 0.385 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 3777 4.38 %
Rwork0.2221 82361 -
obs0.2242 45567 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.41 Å2
Refinement stepCycle: LAST / Resolution: 2.41→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7112 0 2 35 7149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00947261
X-RAY DIFFRACTIONf_angle_d1.11199854
X-RAY DIFFRACTIONf_chiral_restr0.05151104
X-RAY DIFFRACTIONf_plane_restr0.011287
X-RAY DIFFRACTIONf_dihedral_angle_d6.04871025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.440.33111390.34363046X-RAY DIFFRACTION99.66
2.44-2.470.3491380.31763082X-RAY DIFFRACTION99.78
2.47-2.510.34231420.31363002X-RAY DIFFRACTION99.87
2.51-2.540.32761440.31843052X-RAY DIFFRACTION99.91
2.54-2.580.40011450.31463078X-RAY DIFFRACTION99.75
2.58-2.620.32621360.30972987X-RAY DIFFRACTION99.78
2.62-2.660.3541480.30533112X-RAY DIFFRACTION99.94
2.66-2.710.41431400.30553013X-RAY DIFFRACTION99.94
2.71-2.760.3361390.293028X-RAY DIFFRACTION99.91
2.76-2.810.33341440.28993087X-RAY DIFFRACTION99.97
2.81-2.870.36941400.28623046X-RAY DIFFRACTION99.81
2.87-2.930.33131410.26733052X-RAY DIFFRACTION99.94
2.93-30.31311360.25823026X-RAY DIFFRACTION100
3-3.070.32141390.26973055X-RAY DIFFRACTION99.97
3.07-3.160.31611370.27053091X-RAY DIFFRACTION99.97
3.16-3.250.31031390.26213040X-RAY DIFFRACTION100
3.25-3.350.29481410.24823025X-RAY DIFFRACTION99.97
3.35-3.470.31041340.23933082X-RAY DIFFRACTION99.97
3.47-3.610.30031420.25063047X-RAY DIFFRACTION100
3.61-3.780.27561380.22773040X-RAY DIFFRACTION99.94
3.78-3.980.24361460.21393071X-RAY DIFFRACTION99.97
3.98-4.220.21391340.19563059X-RAY DIFFRACTION99.97
4.23-4.550.23181430.18073048X-RAY DIFFRACTION100
4.55-5.010.21281360.18063051X-RAY DIFFRACTION99.94
5.01-5.730.27261370.22143037X-RAY DIFFRACTION99.97
5.73-7.20.29171410.21753061X-RAY DIFFRACTION100
7.2-29.640.19541380.15443043X-RAY DIFFRACTION99.44

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