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- PDB-4ilr: Recognition and Cleavage of a non-structured CRISPR RNA by its Pr... -

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Basic information

Entry
Database: PDB / ID: 4ilr
TitleRecognition and Cleavage of a non-structured CRISPR RNA by its Processing Endoribonuclease Cas6
ComponentsCRISPR-associated endoribonuclease Cas6 2
KeywordsHYDROLASE / RRM / RNA cleavage / RNA
Function / homology
Function and homology information


defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Cas6, N-terminal domain, archaea / Cas6 N-terminal domain / CRISPR-associated protein Cas6, C-terminal / CRISPR-associated endoribonuclease Cas6 / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas6 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.088 Å
AuthorsShao, Y. / Li, H.
CitationJournal: Structure / Year: 2013
Title: Recognition and cleavage of a nonstructured CRISPR RNA by its processing endoribonuclease Cas6.
Authors: Shao, Y. / Li, H.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas6 2


Theoretical massNumber of molelcules
Total (without water)32,6841
Polymers32,6841
Non-polymers00
Water00
1
A: CRISPR-associated endoribonuclease Cas6 2

A: CRISPR-associated endoribonuclease Cas6 2


Theoretical massNumber of molelcules
Total (without water)65,3682
Polymers65,3682
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area2750 Å2
ΔGint-20 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.362, 58.362, 470.998
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CRISPR-associated endoribonuclease Cas6 2


Mass: 32684.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: cas6b, SSO2004 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97WV8, Hydrolases; Acting on ester bonds

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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: 3.54 Å3/Da / Density % sol: 65.28 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 200mM MgCl2, 100mM Tris-Cl (pH 7.6), 32% PEG 400., VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 21, 2012
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→34 Å / Num. all: 10085 / Num. obs: 8986 / % possible obs: 89.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 28.2 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.084 / Net I/σ(I): 42.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 500 / Rsym value: 0.427 / % possible all: 34.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.088→26.772 Å / SU ML: 0.39 / σ(F): 0 / Phase error: 41.2 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2997 834 9.92 %Random
Rwork0.2773 ---
obs0.2795 8411 86.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.088→26.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2225 0 0 0 2225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062267
X-RAY DIFFRACTIONf_angle_d1.0863054
X-RAY DIFFRACTIONf_dihedral_angle_d14.558865
X-RAY DIFFRACTIONf_chiral_restr0.069351
X-RAY DIFFRACTIONf_plane_restr0.004380
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.088-3.28090.4088590.4301587X-RAY DIFFRACTION42
3.2809-3.53370.58951210.41081124X-RAY DIFFRACTION81
3.5337-3.88830.44011590.39061404X-RAY DIFFRACTION97
3.8883-4.44880.37981550.29581399X-RAY DIFFRACTION98
4.4488-5.59650.26421600.2611445X-RAY DIFFRACTION98
5.5965-26.77270.23471800.23031618X-RAY DIFFRACTION99

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