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- PDB-8y7f: Crystal structure of CARF domain-truncated Csx1-Crn2 from Marinit... -

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Basic information

Entry
Database: PDB / ID: 8y7f
TitleCrystal structure of CARF domain-truncated 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 / SAD / Resolution: 2.95 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein
B: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)90,3152
Polymers90,3152
Non-polymers00
Water00
1
A: CRISPR-associated protein
B: CRISPR-associated protein

A: CRISPR-associated protein
B: CRISPR-associated protein


Theoretical massNumber of molelcules
Total (without water)180,6314
Polymers180,6314
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_555-x+1/4,-z+1/4,-y+1/41
Buried area13400 Å2
ΔGint-27 kcal/mol
Surface area65350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.580, 210.580, 210.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein CRISPR-associated protein


Mass: 45157.660 Da / Num. of mol.: 2
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

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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: 4.31 Å3/Da / Density % sol: 71.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Calcium acetate,0.1 M Na cacodylate pH 6.5, 40% PEG 300

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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: 2.95→40.53 Å / Num. obs: 34091 / % possible obs: 100 % / Redundancy: 39.7 % / CC1/2: 0.999 / Net I/σ(I): 19.7
Reflection shellResolution: 2.95→3.06 Å / Num. unique obs: 34091 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PHENIXmodel building
xia2data scaling
PHENIXphasing
xia2data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.95→40.53 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2302 1658 4.86 %
Rwork0.2 --
obs0.2014 34089 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→40.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6023 0 0 0 6023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.301
X-RAY DIFFRACTIONf_dihedral_angle_d5.552781
X-RAY DIFFRACTIONf_chiral_restr0.065933
X-RAY DIFFRACTIONf_plane_restr0.0091017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.040.30811160.26152651X-RAY DIFFRACTION100
3.04-3.130.28161230.24892661X-RAY DIFFRACTION100
3.14-3.250.28931700.25742627X-RAY DIFFRACTION100
3.25-3.380.30151250.24842664X-RAY DIFFRACTION100
3.38-3.530.27351360.21852656X-RAY DIFFRACTION100
3.53-3.720.23941290.20672674X-RAY DIFFRACTION100
3.72-3.950.22941440.19772670X-RAY DIFFRACTION100
3.95-4.250.21391300.18282714X-RAY DIFFRACTION100
4.26-4.680.22611450.1612693X-RAY DIFFRACTION100
4.68-5.360.19241510.1712719X-RAY DIFFRACTION100
5.36-6.740.21591230.22782783X-RAY DIFFRACTION100
6.75-40.530.19371660.17822919X-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)
11.4369-0.44720.30311.11560.1891.57060.14750.2656-0.0472-0.1192-0.22460.19130.0669-0.02870.00030.31860.05620.01260.4014-0.04250.232231.791222.2182-33.7566
21.1731-0.4134-0.37340.34230.04880.84230.0631-0.08620.35790.0222-0.0854-0.0054-0.313-0.1776-0.00040.37780.05830.00960.36480.01550.387826.564447.6702-17.3995
30.85380.20820.25280.7827-0.64140.7135-0.07880.05610.0292-0.03660.0511-0.26250.01840.1247-0.00180.3226-0.0430.10780.31540.01250.359559.039645.5963-14.6142
4-0.01470.2461-0.22221.248-0.43650.8705-0.19230.2834-0.205-0.09590.0470.24630.139-0.1488-0.0730.2272-0.0178-0.00430.5921-0.17180.33941.413722.9692-21.3899
51.05460.1626-0.56990.6548-0.21860.5706-0.1759-0.1923-0.03910.08060.1453-0.0548-0.07080.15830.00010.23530.06080.03220.4387-0.01970.285918.537831.51110.3378
60.94660.1783-0.95621.1554-0.41110.8289-0.0035-0.1134-0.02250.11740.0330.1305-0.0504-0.0519-00.22010.10050.00120.26230.04550.258-10.798943.49879.0019
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 185 through 336 )
2X-RAY DIFFRACTION2chain 'A' and (resid 337 through 438 )
3X-RAY DIFFRACTION3chain 'A' and (resid 439 through 563 )
4X-RAY DIFFRACTION4chain 'B' and (resid 185 through 336 )
5X-RAY DIFFRACTION5chain 'B' and (resid 337 through 437 )
6X-RAY DIFFRACTION6chain 'B' and (resid 438 through 563 )

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