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- PDB-8y75: Crystal structure of the CARF-HTH domain of Csx1-Crn2 from Marini... -

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Basic information

Entry
Database: PDB / ID: 8y75
TitleCrystal structure of the CARF-HTH domain of Csx1-Crn2 from Marinitoga sp.
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 system endoribonuclease Csx1-like / CRISPR system endoribonuclease Csx1, HEPN domain / CRISPR system endoribonuclease Csx1-like domain-containing protein
Function and homology information
Biological speciesMarinitoga sp. 1155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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

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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: CRISPR-associated protein
D: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)209,6844
Polymers209,6844
Non-polymers00
Water4,143230
1
A: CRISPR-associated protein
C: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)104,8422
Polymers104,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5630 Å2
ΔGint-27 kcal/mol
Surface area27390 Å2
MethodPISA
2
B: CRISPR-associated protein

D: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)104,8422
Polymers104,8422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5590 Å2
ΔGint-28 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.884, 193.134, 61.213
Angle α, β, γ (deg.)90.00, 92.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CRISPR-associated protein


Mass: 52421.051 Da / Num. of mol.: 4
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Potassium nitrate pH 6.9, 20% PEG 3350 and 0.2 M Calcium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→38.6 Å / Num. obs: 47810 / % possible obs: 98.08 % / Redundancy: 5.6 % / CC1/2: 0.998 / Net I/σ(I): 14.68
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 4749 / 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: 2.4→38.6 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2568 1997 4.18 %
Rwork0.1958 --
obs0.1983 47810 98.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9984 0 0 230 10214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014
X-RAY DIFFRACTIONf_angle_d2.08
X-RAY DIFFRACTIONf_dihedral_angle_d10.1041301
X-RAY DIFFRACTIONf_chiral_restr0.1081561
X-RAY DIFFRACTIONf_plane_restr0.0231713
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.32221340.25663302X-RAY DIFFRACTION98
2.46-2.530.31491440.24913198X-RAY DIFFRACTION98
2.53-2.60.30071490.25293251X-RAY DIFFRACTION98
2.6-2.680.3161370.2553289X-RAY DIFFRACTION98
2.68-2.780.37531360.2533270X-RAY DIFFRACTION98
2.78-2.890.32181570.23813238X-RAY DIFFRACTION98
2.89-3.020.31851380.2373272X-RAY DIFFRACTION98
3.02-3.180.29551430.22743279X-RAY DIFFRACTION98
3.18-3.380.30581370.22573295X-RAY DIFFRACTION99
3.38-3.640.26051460.20513248X-RAY DIFFRACTION98
3.64-4.010.2431450.18353270X-RAY DIFFRACTION98
4.01-4.590.22121500.15623281X-RAY DIFFRACTION99
4.59-5.770.22531390.16423304X-RAY DIFFRACTION99
5.78-38.60.18051420.15383316X-RAY DIFFRACTION98
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)
13.5257-0.5135-1.35853.39711.05184.1174-0.0255-0.11450.07550.4536-0.0327-0.0151-0.24180.1020.05630.3821-0.0919-0.04280.3172-0.04020.253726.444115.721425.0809
28.3072-0.1838-1.01952.65841.17765.88810.1093-0.0953-0.20110.3432-0.02470.17370.2781-0.1889-0.05060.361-0.11530.03520.2796-0.00380.276521.70038.524717.8882
34.86450.4876-1.50585.1129-0.27823.3636-0.0146-0.2294-0.1862-0.1191-0.0007-0.13320.14390.2130.00720.2538-0.0337-0.00950.29440.04280.272716.5893-19.094513.6625
42.68610.0734-0.1093.0225-0.0143.3649-0.0030.0017-0.2-0.2130.0621-0.1090.51330.133-0.07750.44680.04670.0350.27970.00360.24875.1763-50.88424.8843
51.38590.2003-0.51785.53320.9642.08090.1299-0.03360.44180.09980.03110.4755-0.3459-0.0527-0.11660.39910.02720.04070.42130.0550.4387-8.3086-21.408432.0212
63.6741.4584-0.024.88750.08325.1070.1350.02480.1474-0.4287-0.3342-0.1045-0.190.47580.14560.377-0.0203-0.05520.33990.02460.217524.996918.3369-6.7786
73.1826-0.8149-0.14613.4497-0.8124.11660.02740.2826-0.0063-0.3822-0.12540.4564-0.1342-0.1530.06710.2388-0.0376-0.07280.296-0.06650.350711.104913.2121-3.6077
83.09280.3909-0.39171.3621-2.13843.76040.02980.0143-0.04940.1571-0.1850.06020.05510.39510.15980.2434-0.0217-0.01770.3071-0.01880.236224.316610.26030.897
92.6534-1.28391.65858.1129-3.01673.1891-0.1195-0.0285-0.043-0.44240.277-0.08950.0504-0.2374-0.08960.2746-0.03760.0280.3574-0.05450.375439.8051-5.36561.0819
105.0479-2.0778-0.06356.4675-1.38214.90180.24710.3945-0.7439-0.9316-0.0723-0.69650.7245-0.1205-0.2110.39810.0455-0.05370.4774-0.15720.675749.4668-15.71141.0821
113.154-0.92920.38727.8293-2.72372.68330.175-0.1259-0.18130.2994-0.2812-0.2195-0.30650.09140.18280.251-0.03520.01120.3672-0.05210.295546.3073-3.17567.1116
122.7279-0.27310.18242.186-1.10924.9017-0.11-0.1864-0.16580.4640.08440.23540.34230.09920.00840.56190.09660.07420.31930.03890.2811-1.2031-50.6727-11.0083
130.9799-0.2541-0.12077.364-0.37621.18550.0035-0.3920.3425-0.04060.0718-1.1157-0.17950.3388-0.08520.55190.02870.040.6948-0.1330.600523.245-28.8072-14.6163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 131 )
2X-RAY DIFFRACTION2chain 'A' and (resid 132 through 182 )
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 305 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 173 )
5X-RAY DIFFRACTION5chain 'B' and (resid 174 through 305 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 45 )
7X-RAY DIFFRACTION7chain 'C' and (resid 46 through 117 )
8X-RAY DIFFRACTION8chain 'C' and (resid 118 through 182 )
9X-RAY DIFFRACTION9chain 'C' and (resid 183 through 230 )
10X-RAY DIFFRACTION10chain 'C' and (resid 231 through 275 )
11X-RAY DIFFRACTION11chain 'C' and (resid 276 through 305 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 174 )
13X-RAY DIFFRACTION13chain 'D' and (resid 175 through 304 )

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