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

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Basic information

Entry
Database: PDB / ID: 4ill
TitleRecognition and Cleavage of a non-structured CRISPR RNA by its Processing Endoribonuclease Cas6
Components
  • CRISPR-associated endoribonuclease Cas6 2
  • RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*AP*AP*UP*UP*GP*AP*AP*AP*G)-3')
KeywordsHYDROLASE/RNA / Cas6 / RNA cleavage / RNA / 2'-deoxy modification / U16 / HYDROLASE-RNA complex
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #310 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Alpha-Beta Plaits / Beta Barrel ...Elongation Factor Tu (Ef-tu); domain 3 - #310 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas6 2
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.484 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas6 2
R: RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*AP*AP*UP*UP*GP*AP*AP*AP*G)-3')
B: CRISPR-associated endoribonuclease Cas6 2
C: RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*AP*AP*UP*UP*GP*AP*AP*AP*G)-3')


Theoretical massNumber of molelcules
Total (without water)80,7424
Polymers80,7424
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-52 kcal/mol
Surface area27330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.735, 68.542, 79.831
Angle α, β, γ (deg.)90.00, 119.12, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CRISPR-associated endoribonuclease Cas6 2


Mass: 32684.143 Da / Num. of mol.: 2
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
#2: RNA chain RNA (5'-R(*GP*CP*UP*AP*AP*UP*CP*UP*AP*CP*UP*AP*UP*AP*GP*AP*AP*UP*UP*GP*AP*AP*AP*G)-3')


Mass: 7686.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RNA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
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: 0.9792 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→32 Å / Num. all: 26668 / Num. obs: 24962 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 62 Å2 / Rsym value: 0.093 / Net I/σ(I): 41.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.2 % / Num. unique all: 1812 / Rsym value: 0.511 / % possible all: 54.5

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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: 2.484→32 Å / SU ML: 0.26 / σ(F): 0 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 1969 8.06 %random
Rwork0.2042 ---
all0.22 26668 --
obs0.2071 24441 91.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.484→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 762 0 12 5206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055366
X-RAY DIFFRACTIONf_angle_d1.0677398
X-RAY DIFFRACTIONf_dihedral_angle_d16.5532141
X-RAY DIFFRACTIONf_chiral_restr0.065878
X-RAY DIFFRACTIONf_plane_restr0.005790
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.484-2.54580.3452770.3054808X-RAY DIFFRACTION47
2.5458-2.61470.2979970.28871128X-RAY DIFFRACTION65
2.6147-2.69160.33571270.26881399X-RAY DIFFRACTION80
2.6916-2.77840.30341380.27171601X-RAY DIFFRACTION91
2.7784-2.87770.29921500.27041702X-RAY DIFFRACTION97
2.8777-2.99280.34481560.25481724X-RAY DIFFRACTION98
2.9928-3.1290.27621450.24841717X-RAY DIFFRACTION99
3.129-3.29380.29131520.2291752X-RAY DIFFRACTION100
3.2938-3.50.28061560.23071756X-RAY DIFFRACTION100
3.5-3.76990.2261500.20581769X-RAY DIFFRACTION100
3.7699-4.14880.23021540.1891744X-RAY DIFFRACTION100
4.1488-4.74780.19521540.16941768X-RAY DIFFRACTION100
4.7478-5.97690.20761560.18651780X-RAY DIFFRACTION100
5.9769-34.8890.21311570.18491824X-RAY DIFFRACTION99

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