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- PDB-5wlh: Crystal structure of LbaCas13a H328A (C2c2) bound to pre-crRNA (2... -

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Basic information

Entry
Database: PDB / ID: 5wlh
TitleCrystal structure of LbaCas13a H328A (C2c2) bound to pre-crRNA (24-nt spacer)
Components
  • LbaCas13a H328A (C2c2)
  • pre-crRNA
KeywordsRNA BINDING PROTEIN/RNA / Nuclease RNA binding protein / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homologyIODIDE ION / RNA / RNA (> 10) / LbaCas13a H328A (C2c2)
Function and homology information
Biological speciesLachnospiraceae bacterium NK4A179 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.80001033182 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
DepositionJul 26, 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

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Assembly

Deposited unit
A: LbaCas13a H328A (C2c2)
B: pre-crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,31923
Polymers186,6892
Non-polymers2,63021
Water13,781765
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, homology, PDB code: 5W1H, 5W1I, 5WTK
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15060 Å2
ΔGint-72 kcal/mol
Surface area54610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.842, 92.213, 115.858
Angle α, β, γ (deg.)90.000, 92.425, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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

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Components

#1: Protein LbaCas13a H328A (C2c2)


Mass: 169125.641 Da / Num. of mol.: 1 / Mutation: H328A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium NK4A179 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TCH1*PLUS
#2: RNA chain pre-crRNA


Mass: 17563.594 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium NK4A179 (bacteria)
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 765 / 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: 42.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium iodide, 20 % 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: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.71→47.116494566 Å / Num. obs: 162397 / % possible obs: 93.3 % / Redundancy: 5 % / Biso Wilson estimate: 30.1855803653 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.025 / Rrim(I) all: 0.057 / Χ2: 1.18 / Net I/σ(I): 15.2 / Num. measured all: 807018 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.71-1.744.41.1742146748590.5020.6031.3251.256.8
9.36-116.5950.028553811140.9990.0140.0315599.1

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WIH

5wih


Resolution: 1.80001033182→47.116494566 Å / SU ML: 0.215930613219 / Cross valid method: FREE R-VALUE / σ(F): 1.35143778714 / Phase error: 23.5449843848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.217315192527 6909 4.8377271295 %
Rwork0.18418885485 135906 -
obs0.185842735198 142815 97.3550564096 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.3534789683 Å2
Refinement stepCycle: LAST / Resolution: 1.80001033182→47.116494566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10654 912 26 765 12357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063755458823211921
X-RAY DIFFRACTIONf_angle_d0.82733280600416237
X-RAY DIFFRACTIONf_chiral_restr0.04969054783391761
X-RAY DIFFRACTIONf_plane_restr0.004525798675131930
X-RAY DIFFRACTIONf_dihedral_angle_d7.96974588399808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.3103461219412090.2610637754454379X-RAY DIFFRACTION94.3256578947
1.8205-1.84190.2812837696012350.2516314629254487X-RAY DIFFRACTION95.6063980563
1.8419-1.86430.2933915282132340.2454506287374360X-RAY DIFFRACTION95.9081419624
1.8643-1.88790.3041594436311970.2367997161764500X-RAY DIFFRACTION96.1711711712
1.8879-1.91280.2880832910382270.2238555943754467X-RAY DIFFRACTION96.1885245902
1.9128-1.9390.2555355555732170.2249624665694458X-RAY DIFFRACTION96.2726523888
1.939-1.96670.2649698268092460.2133128874794477X-RAY DIFFRACTION96.5059256232
1.9667-1.9960.2802217732442050.2123829899154475X-RAY DIFFRACTION96.4550700742
1.996-2.02720.2495295851531950.2081754258824487X-RAY DIFFRACTION96.4962901896
2.0272-2.06050.229295637962220.2047775099824548X-RAY DIFFRACTION96.9315179841
2.0605-2.0960.2326321438082260.1970793793734490X-RAY DIFFRACTION96.8775677896
2.096-2.13410.2340297548882250.198218165484458X-RAY DIFFRACTION96.9966859983
2.1341-2.17520.2496683412762290.1933403808734515X-RAY DIFFRACTION97.2330395573
2.1752-2.21960.229407680262320.199223011734535X-RAY DIFFRACTION97.1667346107
2.2196-2.26780.2389642635642420.1996296988014529X-RAY DIFFRACTION97.4468954248
2.2678-2.32060.2809103774712230.1962749028414510X-RAY DIFFRACTION97.3667969554
2.3206-2.37860.2420580718912120.1952268546634530X-RAY DIFFRACTION97.6322833025
2.3786-2.44290.2227316071672220.1858414674944544X-RAY DIFFRACTION97.7039770398
2.4429-2.51480.2584617849492480.1963382126734550X-RAY DIFFRACTION97.8784169727
2.5148-2.5960.2422780148722440.1972341895924579X-RAY DIFFRACTION97.9488220959
2.596-2.68870.232474527412440.1974535448024525X-RAY DIFFRACTION98.046875
2.6887-2.79640.247386439582200.19314212264545X-RAY DIFFRACTION97.9445015416
2.7964-2.92360.2301192815242180.1969610430794579X-RAY DIFFRACTION98.3394833948
2.9236-3.07770.2375299981442090.1887723292274625X-RAY DIFFRACTION98.2919886133
3.0777-3.27050.2104513156482390.1920785569474596X-RAY DIFFRACTION98.5126324368
3.2705-3.5230.2302182702852770.1792103017014582X-RAY DIFFRACTION98.6999796872
3.523-3.87740.1715653911132790.1603865486434561X-RAY DIFFRACTION98.8764044944
3.8774-4.43810.1910397764142490.1547696365484616X-RAY DIFFRACTION98.701562183
4.4381-5.590.1763877430252240.1531937490654661X-RAY DIFFRACTION99.0470397405
5.59-47.13260.1888326466992600.1802393338944738X-RAY DIFFRACTION98.9311163895

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