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- PDB-5w1h: Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (24-n... -

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Basic information

Entry
Database: PDB / ID: 5w1h
TitleCrystal structure of LbaCas13a (C2c2) bound to mature crRNA (24-nt spacer)
Components
  • LbaCas13a (C2c2)
  • mature crRNA
KeywordsRNA BINDING PROTEIN/RNA / Nuclease RNA binding protein / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology: / endonuclease activity / defense response to virus / hydrolase activity / RNA binding / IODIDE ION / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesLachnospiraceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.99 Å
AuthorsKnott, G.J. / Doudna, J.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme.
Authors: Knott, G.J. / East-Seletsky, A. / Cofsky, J.C. / Holton, J.M. / Charles, E. / O'Connell, M.R. / Doudna, J.A.
History
DepositionJun 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 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: LbaCas13a (C2c2)
B: mature crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,27728
Polymers186,0822
Non-polymers3,19526
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, PDB code: 5WTK
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-78 kcal/mol
Surface area55970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.842, 92.213, 115.858
Angle α, β, γ (deg.)90.00, 92.42, 90.00
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1513-

IOD

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Components

#1: Protein LbaCas13a (C2c2)


Mass: 169192.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium (bacteria) / Gene: NK4A179 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / Variant (production host): 2DE3 / References: UniProt: A0A2D0TCG9*PLUS
#2: RNA chain mature crRNA


Mass: 16889.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lachnospiraceae bacterium (bacteria)
#3: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium iodide, 20 - 25 % PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Cryostream
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.99→47.12 Å / Num. obs: 107265 / % possible obs: 98.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 32.09 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 15.2
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 6 % / Rmerge(I) obs: 0.841 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575-000refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
SHELXCDphasing
SHELXDEphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.99→47.12 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.87
RfactorNum. reflection% reflectionSelection details
Rfree0.216 5242 4.89 %Random
Rwork0.185 ---
obs0.187 107256 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.6 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10760 886 41 812 12499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00211972
X-RAY DIFFRACTIONf_angle_d0.48216294
X-RAY DIFFRACTIONf_dihedral_angle_d16.1317156
X-RAY DIFFRACTIONf_chiral_restr0.0381766
X-RAY DIFFRACTIONf_plane_restr0.0031939
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.01260.29061460.25783041X-RAY DIFFRACTION88
2.0126-2.03630.26871360.24363287X-RAY DIFFRACTION95
2.0363-2.06110.24851620.23043349X-RAY DIFFRACTION97
2.0611-2.08720.28251680.22543362X-RAY DIFFRACTION98
2.0872-2.11470.28471660.22443388X-RAY DIFFRACTION99
2.1147-2.14370.25521810.21133375X-RAY DIFFRACTION98
2.1437-2.17430.29761760.20993366X-RAY DIFFRACTION99
2.1743-2.20680.26751760.20443405X-RAY DIFFRACTION99
2.2068-2.24120.24431950.1993364X-RAY DIFFRACTION99
2.2412-2.2780.21621620.19863391X-RAY DIFFRACTION99
2.278-2.31730.2521670.20013432X-RAY DIFFRACTION99
2.3173-2.35940.25791610.2033402X-RAY DIFFRACTION99
2.3594-2.40480.23621570.20523393X-RAY DIFFRACTION99
2.4048-2.45390.27641780.19623431X-RAY DIFFRACTION99
2.4539-2.50720.24191880.20023401X-RAY DIFFRACTION99
2.5072-2.56550.2511780.2073385X-RAY DIFFRACTION99
2.5655-2.62970.2571980.19763391X-RAY DIFFRACTION99
2.6297-2.70080.24281730.20263443X-RAY DIFFRACTION99
2.7008-2.78020.22691590.19673424X-RAY DIFFRACTION99
2.7802-2.870.26361790.19793409X-RAY DIFFRACTION100
2.87-2.97250.22011440.19613481X-RAY DIFFRACTION99
2.9725-3.09150.2381630.18893453X-RAY DIFFRACTION100
3.0915-3.23220.20431680.19353420X-RAY DIFFRACTION100
3.2322-3.40260.23922000.18733458X-RAY DIFFRACTION100
3.4026-3.61570.19522200.17483372X-RAY DIFFRACTION100
3.6157-3.89470.18912110.16033427X-RAY DIFFRACTION100
3.8947-4.28640.18971970.16113426X-RAY DIFFRACTION100
4.2864-4.90610.16631610.15413517X-RAY DIFFRACTION100
4.9061-6.1790.2111850.17453474X-RAY DIFFRACTION100
6.179-47.12970.16731870.17113547X-RAY DIFFRACTION100

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