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- PDB-8y7g: Crystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in... -

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Basic information

Entry
Database: PDB / ID: 8y7g
TitleCrystal structure of the Marinitoga sp. Csx1-Crn2 H495A mutant in complex with cyclic-tetraadenylate (cA4)
Components
  • CRISPR-associated protein
  • RNA (5'-R(P*AP*A)-3')
  • RNA (5'-R(P*AP*AP*AP*A)-3')
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 / ACETATE ION / RNA / CRISPR-associated protein
Function and homology information
Biological speciesMarinitoga sp. 1155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsZhang, D. / Yuan, C. / Lin, Z.
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 4, 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _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: CRISPR-associated protein
B: CRISPR-associated protein
C: RNA (5'-R(P*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*A)-3')
E: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5407
Polymers135,4215
Non-polymers1182
Water00
1
A: CRISPR-associated protein
B: CRISPR-associated protein
C: RNA (5'-R(P*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*A)-3')
E: RNA (5'-R(P*AP*A)-3')
hetero molecules

A: CRISPR-associated protein
B: CRISPR-associated protein
C: RNA (5'-R(P*AP*AP*AP*A)-3')
D: RNA (5'-R(P*AP*A)-3')
E: RNA (5'-R(P*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,07914
Polymers270,84310
Non-polymers2364
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_465-x-1,-y+1,z1
Buried area32510 Å2
ΔGint-101 kcal/mol
Surface area87110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.496, 119.564, 196.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-601-

ACT

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Components

#1: Protein CRISPR-associated protein


Mass: 66461.359 Da / Num. of mol.: 2 / Mutation: H495A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinitoga sp. 1155 (bacteria) / Gene: X274_06335 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2SHM8
#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.) Marinitoga sp. 1155 (bacteria)
#3: RNA chain RNA (5'-R(P*AP*A)-3')


Mass: 613.454 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Marinitoga sp. 1155 (bacteria)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.0, 10% 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: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.15→52.79 Å / Num. obs: 30656 / % possible obs: 99.74 % / Redundancy: 13.2 % / CC1/2: 0.997 / Net I/σ(I): 13.88
Reflection shellResolution: 3.15→3.27 Å / Num. unique obs: 30656 / CC1/2: 0.999

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHENIXmodel building
autoPROCdata scaling
PHENIXphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→52.79 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2804 1997 6.51 %
Rwork0.2124 --
obs0.2168 30656 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→52.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8691 176 8 0 8875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.377
X-RAY DIFFRACTIONf_dihedral_angle_d10.5591235
X-RAY DIFFRACTIONf_chiral_restr0.0671405
X-RAY DIFFRACTIONf_plane_restr0.0091498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.40211390.31622018X-RAY DIFFRACTION100
3.23-3.320.35891410.2732020X-RAY DIFFRACTION100
3.32-3.420.311400.25142004X-RAY DIFFRACTION100
3.42-3.530.34811400.25122018X-RAY DIFFRACTION100
3.53-3.650.3141420.25712021X-RAY DIFFRACTION100
3.65-3.80.31711400.22632005X-RAY DIFFRACTION100
3.8-3.970.34441410.21712030X-RAY DIFFRACTION100
3.97-4.180.25741420.20942037X-RAY DIFFRACTION100
4.18-4.440.27541410.18662023X-RAY DIFFRACTION100
4.44-4.780.23611440.16882054X-RAY DIFFRACTION100
4.79-5.270.19381430.17772069X-RAY DIFFRACTION100
5.27-6.030.30821440.2212068X-RAY DIFFRACTION100
6.03-7.590.31821470.24422103X-RAY DIFFRACTION100
7.59-52.790.22861530.17782189X-RAY DIFFRACTION99
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)
11.0635-0.3158-0.00280.1427-0.1170.23570.51510.6599-0.0603-1.0036-0.30510.14110.1161-0.314-0.18233.1335-0.2303-0.16171.0302-0.05760.92-46.405260.7834-78.0863
20.89090.8911-0.31411.908-0.3980.8539-0.29550.2258-0.2375-0.89560.2982-0.1296-0.09310.37410.08440.7432-0.34870.05980.3558-0.06230.9389-43.11637.4076-27.8224
31.23830.08760.6971.6742-0.03113.8863-0.0783-0.7946-0.34111.22280.11370.04840.74130.0335-0.09521.10520.32010.05180.72040.12370.8717-37.277250.39247.242
40.61210.93840.95682.34421.4551.4482-0.0721-0.08890.1495-0.0405-0.26920.6138-0.0447-0.47980.2330.3617-0.0326-0.02710.2241-0.10171.1432-58.48149.831-1.3311
56.9947-4.09190.33385.31880.37836.5713-1.14392.2238-0.3455-0.7566-0.48990.80771.2470.3151.62623.2561-0.3997-0.00541.9624-0.26751.0273-38.914663.7287-97.0111
62.52630.86671.97841.59311.59162.27660.1174-1.5476-0.12340.7951-0.77070.05530.787-0.69770.60792.87840.40140.1212.2047-0.03170.8058-33.290359.178370.4351
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 298 )
2X-RAY DIFFRACTION2chain 'A' and (resid 299 through 563 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 336 )
4X-RAY DIFFRACTION4chain 'B' and (resid 337 through 563 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 2 )
6X-RAY DIFFRACTION6chain 'E' and (resid 1 through 2 )

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