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- PDB-3pkm: Crystal structure of Cas6 with its substrate RNA -

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Basic information

Entry
Database: PDB / ID: 3pkm
TitleCrystal structure of Cas6 with its substrate RNA
Components
  • 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'
  • 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'
  • CRISPR-associated endoribonuclease Cas6
KeywordsHYDROLASE/RNA / Cas6 / CRISPR / endonuclease / Ferridoxin fold / CRISPR processing endonuclease / repeat RNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
: / CRISPR-associated protein Cas6, N-terminal / CRISPR associated protein Cas6, C-terminal / CRISPR-associated protein Cas6, N-terminal domain superfamily / Alpha-Beta Plaits - #1890 / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / CRISPR-associated endoribonuclease Cas6
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.103 Å
AuthorsWang, R. / Preamplume, G. / Li, H.
CitationJournal: Structure / Year: 2011
Title: Interaction of the Cas6 Riboendonuclease with CRISPR RNAs: Recognition and Cleavage.
Authors: Wang, R. / Preamplume, G. / Terns, M.P. / Terns, R.M. / Li, H.
History
DepositionNov 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated endoribonuclease Cas6
X: CRISPR-associated endoribonuclease Cas6
G: 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'
R: 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)68,6094
Polymers68,6094
Non-polymers00
Water00
1
A: CRISPR-associated endoribonuclease Cas6
G: 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)34,4692
Polymers34,4692
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
X: CRISPR-associated endoribonuclease Cas6
R: 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'


Theoretical massNumber of molelcules
Total (without water)34,1402
Polymers34,1402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.557, 96.557, 165.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26
17
27

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain X and resid 6:24
211chain A and resid 6:24
112chain X and resid 25:54
212chain A and resid 25:54
113chain X and resid 55:74
213chain A and resid 55:74
114chain X and resid 75:127
214chain A and resid 75:127
115chain X and resid 128:151
215chain A and resid 128:151
116chain X and resid 152:245
216chain A and resid 152:245
117chain G and resid 2:10
217chain R and resid 2:10

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

#1: Protein CRISPR-associated endoribonuclease Cas6


Mass: 31315.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: cas6, PF1131 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8U1S4, Hydrolases; Acting on ester bonds
#2: RNA chain 5'-R(*AP*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'


Mass: 3153.957 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: RNA chain 5'-R(P*UP*UP*AP*CP*AP*AP*UP*AP*A)-3'


Mass: 2824.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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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: 3.25 Å3/Da / Density % sol: 62.11 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 mM MgCl2, 50 mM NaHepes (pH7.0), 1.4 M Ammonium Sulfate, 4% polypropylene Glycol 400 (p400), 20 mM NiCl2, and 100 mM NaCl, vapor diffusion, hanging drop, temperature 303.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.5418 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 21, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 18186 / Num. obs: 15227 / % possible obs: 83.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.4
Reflection shellResolution: 3.2→3.3 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3.103→46.347 Å / SU ML: 0.53 / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3176 2217 10.24 %RANDOM
Rwork0.2759 ---
obs0.3085 21660 69.38 %-
all-31219 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.853 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-43.5926 Å20 Å2-0 Å2
2--43.5926 Å20 Å2
3----64.2769 Å2
Refinement stepCycle: LAST / Resolution: 3.103→46.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3816 379 0 0 4195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144384
X-RAY DIFFRACTIONf_angle_d2.1865998
X-RAY DIFFRACTIONf_dihedral_angle_d24.0181680
X-RAY DIFFRACTIONf_chiral_restr0.151644
X-RAY DIFFRACTIONf_plane_restr0.01687
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11X101X-RAY DIFFRACTIONPOSITIONAL
12A101X-RAY DIFFRACTIONPOSITIONAL0.056
21X251X-RAY DIFFRACTIONPOSITIONAL
22A251X-RAY DIFFRACTIONPOSITIONAL0.44
31X161X-RAY DIFFRACTIONPOSITIONAL
32A161X-RAY DIFFRACTIONPOSITIONAL0.48
41X428X-RAY DIFFRACTIONPOSITIONAL
42A428X-RAY DIFFRACTIONPOSITIONAL1.082
51X148X-RAY DIFFRACTIONPOSITIONAL
52A148X-RAY DIFFRACTIONPOSITIONAL0.646
61X760X-RAY DIFFRACTIONPOSITIONAL
62A760X-RAY DIFFRACTIONPOSITIONAL0.805
71G189X-RAY DIFFRACTIONPOSITIONAL
72R189X-RAY DIFFRACTIONPOSITIONAL0.043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1032-3.17070.5817670.4714492X-RAY DIFFRACTION29
3.1707-3.24440.4963640.377599X-RAY DIFFRACTION34
3.2444-3.32550.4742900.4265707X-RAY DIFFRACTION41
3.3255-3.41540.3938990.3845833X-RAY DIFFRACTION48
3.4154-3.51590.47081110.4121964X-RAY DIFFRACTION56
3.5159-3.62930.4181080.3547983X-RAY DIFFRACTION55
3.6293-3.7590.39451350.35831204X-RAY DIFFRACTION69
3.759-3.90940.37341320.31271212X-RAY DIFFRACTION69
3.9094-4.08720.3681430.28371278X-RAY DIFFRACTION74
4.0872-4.30250.31291600.27661386X-RAY DIFFRACTION79
4.3025-4.57190.30411690.26671506X-RAY DIFFRACTION85
4.5719-4.92450.32021730.2481568X-RAY DIFFRACTION89
4.9245-5.41940.2961920.24681598X-RAY DIFFRACTION92
5.4194-6.2020.34221720.27891669X-RAY DIFFRACTION94
6.202-7.80790.30962000.29021702X-RAY DIFFRACTION98
7.8079-46.35180.27362020.28811742X-RAY DIFFRACTION99

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