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- PDB-8y6z: Crystal structure of the Marinitoga sp. Csx1-Crn2 fusion ribonucl... -

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Basic information

Entry
Database: PDB / ID: 8y6z
TitleCrystal structure of the Marinitoga sp. Csx1-Crn2 fusion ribonuclease of type III CRISPR
ComponentsCRISPR-associated protein
KeywordsHYDROLASE / type III CRISPR / self-limiting ribonuclease / ring nuclease / Csx1 / Crn2.
Function / homologySTIV B116-like / STIV B116-like superfamily / STIV B116-like / CRISPR-associated protein DxTHG, conserved site / CRISPR-associated protein
Function and homology information
Biological speciesMarinitoga sp. 1155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.65 Å
AuthorsZhang, D. / Yuan, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971222 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural insight into the Csx1-Crn2 fusion self-limiting ribonuclease of type III CRISPR system.
Authors: Zhang, D. / Du, L. / Gao, H. / Yuan, C. / Lin, Z.
History
DepositionFeb 3, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)66,5281
Polymers66,5281
Non-polymers00
Water00
1
B: CRISPR-associated protein

B: CRISPR-associated protein

B: CRISPR-associated protein

B: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)266,1144
Polymers266,1144
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area20300 Å2
ΔGint-111 kcal/mol
Surface area97590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.330, 230.330, 59.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein CRISPR-associated protein


Mass: 66528.430 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinitoga sp. 1155 (bacteria) / Gene: X274_06335 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2SHM8
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: 3.41 Å3/Da / Density % sol: 63.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.6, 8% w/v Polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.65→38.39 Å / Num. obs: 10761 / % possible obs: 99.8 % / Redundancy: 34.1 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 22.3
Reflection shellResolution: 3.65→3.78 Å / Num. unique obs: 1046 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHENIXmodel building
xia2data scaling
PHENIXphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.65→38.39 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2348 549 5.1 %
Rwork0.2112 --
obs0.2125 10761 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.65→38.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4198 0 0 0 4198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.674
X-RAY DIFFRACTIONf_dihedral_angle_d5.768552
X-RAY DIFFRACTIONf_chiral_restr0.046660
X-RAY DIFFRACTIONf_plane_restr0.004713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.65-4.020.23531190.22282490X-RAY DIFFRACTION100
4.02-4.60.23841570.2132491X-RAY DIFFRACTION100
4.6-5.790.24681240.2192549X-RAY DIFFRACTION100
5.79-38.390.22841490.20372682X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03770.67062.00614.9734-0.70543.6190.28490.3545-0.0435-0.4586-0.4138-0.2020.1130.12210.12480.91520.21870.18510.87960.00440.472940.55512.965-11.4497
23.83031.3594-0.76272.39210.21550.31570.7414-0.12030.15680.4505-0.3121-0.9108-0.21120.4043-0.37070.9871-0.0320.00441.56580.00131.609691.287618.43487.9398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 204 )
2X-RAY DIFFRACTION2chain 'B' and (resid 205 through 563 )

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