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- PDB-5wqe: Crystal structure of Alicyclobacillus acidoterrestris C2c1 in com... -

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Basic information

Entry
Database: PDB / ID: 5wqe
TitleCrystal structure of Alicyclobacillus acidoterrestris C2c1 in complex with single-guide RNA at 3.1 Angstrom resolution
Components
  • CRISPR-associated endonuclease C2c1
  • RNA (60-MER)
KeywordsRNA BINDING PROTEIN / CRISPR-Cas endonuclease / Recognition lobe / Nuclease lobe
Function / homologydefense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / RNA / RNA (> 10) / RNA (> 100) / CRISPR-associated endonuclease Cas12b
Function and homology information
Biological speciesAlicyclobacillus acidoterrestris (bacteria)
Alicyclobacillus acidoterrestris ATCC 49025 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.126 Å
AuthorsLiu, L. / Wang, Y.L.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China91440201 China
National Natural Science Foundation of China31571335 China
National Natural Science Foundation of China31400640 China
Ministry of Science and Technology (China)2014CB910102 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010203 China
CitationJournal: Mol. Cell / Year: 2017
Title: C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism
Authors: Liu, L. / Chen, P. / Wang, M. / Li, X. / Wang, J. / Yin, M. / Wang, Y.
History
DepositionNov 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2017Group: Database references
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease C2c1
B: RNA (60-MER)


Theoretical massNumber of molelcules
Total (without water)169,2452
Polymers169,2452
Non-polymers00
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-46 kcal/mol
Surface area56990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)194.554, 129.836, 84.001
Angle α, β, γ (deg.)90.00, 110.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CRISPR-associated endonuclease C2c1 / AacC2c1


Mass: 132877.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidoterrestris (bacteria)
Strain: ATCC 49025 / DSM 3922 / CIP 106132 / NCIMB 13137 / GD3B
Gene: c2c1, N007_06525 / Production host: Escherichia coli (E. coli)
References: UniProt: T0D7A2, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (60-MER)


Mass: 36367.691 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Alicyclobacillus acidoterrestris ATCC 49025 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.95 Å3/Da / Density % sol: 58.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M LiCl and 16% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 27598 / % possible obs: 99.6 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 14.3
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data processing
RefinementMethod to determine structure: SAD / Resolution: 3.126→48.642 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2681 1340 4.86 %
Rwork0.2376 --
obs0.2391 27598 79.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.126→48.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7988 1278 0 42 9308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139580
X-RAY DIFFRACTIONf_angle_d1.89313227
X-RAY DIFFRACTIONf_dihedral_angle_d25.8493709
X-RAY DIFFRACTIONf_chiral_restr0.1291472
X-RAY DIFFRACTIONf_plane_restr0.0081505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1262-3.23790.4058190.2996532X-RAY DIFFRACTION16
3.2379-3.36750.3654510.29981132X-RAY DIFFRACTION34
3.3675-3.52070.35051060.29181980X-RAY DIFFRACTION60
3.5207-3.70630.29691320.26842766X-RAY DIFFRACTION84
3.7063-3.93840.27431780.24953264X-RAY DIFFRACTION99
3.9384-4.24230.23261710.22723294X-RAY DIFFRACTION100
4.2423-4.66890.2281870.20353276X-RAY DIFFRACTION99
4.6689-5.34380.22981780.20583305X-RAY DIFFRACTION100
5.3438-6.72980.29111580.24163332X-RAY DIFFRACTION100
6.7298-48.64770.27451600.23623377X-RAY DIFFRACTION100

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