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- PDB-5w1i: Crystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-n... -

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Basic information

Entry
Database: PDB / ID: 5w1i
TitleCrystal structure of LbaCas13a (C2c2) bound to mature crRNA (20-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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKnott, G.J. / Doudna, J.A.
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 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: mature crRNA
A: LbaCas13a (C2c2)
D: mature crRNA
C: LbaCas13a (C2c2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)374,19420
Polymers372,1644
Non-polymers2,03016
Water20,5911143
1
B: mature crRNA
A: LbaCas13a (C2c2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,8438
Polymers186,0822
Non-polymers7616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11790 Å2
ΔGint-66 kcal/mol
Surface area56980 Å2
MethodPISA
2
D: mature crRNA
C: LbaCas13a (C2c2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,35112
Polymers186,0822
Non-polymers1,26910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-67 kcal/mol
Surface area57590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.780, 89.212, 116.306
Angle α, β, γ (deg.)86.14, 86.97, 66.16
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN 'B' AND (RESID -27 THROUGH 6 OR (RESID 9...
211(CHAIN 'D' AND (RESID -27 THROUGH 7 OR (RESID 10...
112(CHAIN 'A' AND (RESID 14 THROUGH 1076 OR RESID 1079 THROUGH 1378))
212(CHAIN 'C' AND (RESID 14 THROUGH 71 OR RESID 79...

NCS ensembles :
ID
1
2

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Components

#1: RNA chain mature crRNA


Mass: 16889.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Lachnospiraceae bacterium (bacteria)
#2: Protein LbaCas13a (C2c2)


Mass: 169192.703 Da / Num. of mol.: 2
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
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1143 / 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: 2.26 Å3/Da / Density % sol: 45.53 %
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
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS3 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: 2.2→48.57 Å / Num. obs: 161267 / % possible obs: 97.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.466 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.31data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W1H

5w1h


Resolution: 2.2→48.42 Å / SU ML: 0.295 / Cross valid method: FREE R-VALUE / σ(F): 1.959 / Phase error: 25.872
RfactorNum. reflection% reflection
Rfree0.233 2014 1.249 %
Rwork0.197 --
obs0.197 161242 97.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 44.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21444 1642 16 1143 24245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223687
X-RAY DIFFRACTIONf_angle_d0.41532210
X-RAY DIFFRACTIONf_dihedral_angle_d16.06114170
X-RAY DIFFRACTIONf_chiral_restr0.0363489
X-RAY DIFFRACTIONf_plane_restr0.0023855
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDType
11BX-RAY DIFFRACTIONPOSITIONAL
12DX-RAY DIFFRACTIONPOSITIONAL
21AX-RAY DIFFRACTIONPOSITIONAL
22CX-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.35971530.289711280X-RAY DIFFRACTION97
2.255-2.3160.27371480.27111279X-RAY DIFFRACTION97
2.316-2.38410.31071320.256611274X-RAY DIFFRACTION97
2.3841-2.46110.30111460.247411327X-RAY DIFFRACTION97
2.4611-2.5490.31961480.244511362X-RAY DIFFRACTION97
2.549-2.65110.29631320.23611284X-RAY DIFFRACTION97
2.6511-2.77170.30981570.231911451X-RAY DIFFRACTION98
2.7717-2.91790.25131410.218311351X-RAY DIFFRACTION98
2.9179-3.10060.24211430.207811443X-RAY DIFFRACTION98
3.1006-3.340.22331420.211452X-RAY DIFFRACTION98
3.34-3.6760.21961400.183211423X-RAY DIFFRACTION98
3.676-4.20770.19821460.165211456X-RAY DIFFRACTION98
4.2077-5.30020.17631340.154311434X-RAY DIFFRACTION98
5.3002-48.43010.19911520.171611412X-RAY DIFFRACTION98

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