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- PDB-5wtk: Crystal structure of RNP complex -

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Basic information

Entry
Database: PDB / ID: 5wtk
TitleCrystal structure of RNP complex
Components
  • CRISPR-associated endoribonuclease C2c2
  • RNA (58-MER)
KeywordsHYDROLASE/RNA / HYDROLASE-RNA complex
Function / homology: / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / RNA / RNA (> 10) / CRISPR-associated endoribonuclease Cas13a
Function and homology information
Biological speciesLeptotrichia shahii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.651 Å
AuthorsLiu, L. / Wang, Y.
CitationJournal: Cell / Year: 2017
Title: Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities
Authors: Liu, L. / Li, X. / Wang, J. / Wang, M. / Chen, P. / Yin, M. / Li, J. / Sheng, G. / Wang, Y.
History
DepositionDec 13, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: CRISPR-associated endoribonuclease C2c2
B: RNA (58-MER)


Theoretical massNumber of molelcules
Total (without water)186,1582
Polymers186,1582
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-52 kcal/mol
Surface area61590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.589, 137.051, 153.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR-associated endoribonuclease C2c2 / EndoRNase / LshC2c2


Mass: 167624.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia shahii (strain DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37) (bacteria)
Strain: DSM 19757 / CCUG 47503 / CIP 107916 / JCM 16776 / LB37
Gene: c2c2 / Production host: Escherichia coli (E. coli)
References: UniProt: P0DOC6, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (58-MER)


Mass: 18533.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Leptotrichia shahii (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium malonate, 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 53055 / % possible obs: 98.5 % / Redundancy: 4.6 % / Net I/σ(I): 13.4
Reflection shellRmerge(I) obs: 0.625

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data processing
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WTJ

5wtj


Resolution: 2.651→40.405 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 33.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2716 2621 4.94 %
Rwork0.2587 --
obs0.2594 53055 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.651→40.405 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9757 849 0 65 10671
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01210855
X-RAY DIFFRACTIONf_angle_d1.58414807
X-RAY DIFFRACTIONf_dihedral_angle_d26.2134181
X-RAY DIFFRACTIONf_chiral_restr0.1721700
X-RAY DIFFRACTIONf_plane_restr0.0081748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6507-2.69880.42831470.41392546X-RAY DIFFRACTION96
2.6988-2.75070.44841260.38482554X-RAY DIFFRACTION97
2.7507-2.80690.37111280.36742591X-RAY DIFFRACTION97
2.8069-2.86790.38311420.35872575X-RAY DIFFRACTION97
2.8679-2.93460.3361390.34212577X-RAY DIFFRACTION97
2.9346-3.00790.35681210.33092608X-RAY DIFFRACTION98
3.0079-3.08920.30841490.30632608X-RAY DIFFRACTION98
3.0892-3.18010.31891230.29352647X-RAY DIFFRACTION99
3.1801-3.28270.33371500.27812633X-RAY DIFFRACTION99
3.2827-3.40.28741310.26772651X-RAY DIFFRACTION99
3.4-3.5360.27141400.25442666X-RAY DIFFRACTION99
3.536-3.69690.26581290.24132667X-RAY DIFFRACTION99
3.6969-3.89160.27411400.23652669X-RAY DIFFRACTION99
3.8916-4.13520.27981220.23472735X-RAY DIFFRACTION100
4.1352-4.45410.23291470.21852663X-RAY DIFFRACTION100
4.4541-4.90170.22551210.20922752X-RAY DIFFRACTION100
4.9017-5.60940.24351570.2262709X-RAY DIFFRACTION100
5.6094-7.06110.2911580.27962747X-RAY DIFFRACTION100
7.0611-40.40970.20181510.22572836X-RAY DIFFRACTION98

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