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- PDB-5id6: Structure of Cpf1/RNA Complex -

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Basic information

Entry
Database: PDB / ID: 5id6
TitleStructure of Cpf1/RNA Complex
Components
  • Cpf1
  • RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')
KeywordsHYDROLASE
Function / homologyCRISPR-associated endonuclease Cas12a / Cas12a, REC1 domain / Cas12a, RuvC nuclease domain / Cas12a, nuclease domain / Alpha helical recognition lobe domain / Nuclease domain / RuvC nuclease domain / Cpf1
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.382 Å
AuthorsDong, D. / Ren, K. / Qiu, X. / Wang, J. / Huang, Z.
CitationJournal: Nature / Year: 2016
Title: The crystal structure of Cpf1 in complex with CRISPR RNA
Authors: Dong, D. / Ren, K. / Qiu, X. / Zheng, J. / Guo, M. / Guan, X. / Liu, H. / Li, N. / Zhang, B. / Yang, D. / Ma, C. / Wang, S. / Wu, D. / Ma, Y. / Fan, S. / Wang, J. / Gao, N. / Huang, Z.
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cpf1
G: RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,8414
Polymers150,7932
Non-polymers492
Water1086
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-63 kcal/mol
Surface area59820 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)168.352, 83.011, 124.086
Angle α, β, γ (deg.)90.00, 106.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cpf1 /


Mass: 144132.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A182DWE3*PLUS
#2: RNA chain RNA (5'-R(P*AP*AP*UP*UP*UP*CP*UP*AP*CP*UP*AP*AP*GP*UP*GP*UP*AP*GP*AP*UP*C)-3')


Mass: 6659.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.16 M Magnesium acetate, 18%(w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97776 Å
DetectorType: CCD pilatus CBF / Detector: CCD / Date: Jan 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97776 Å / Relative weight: 1
ReflectionResolution: 2.38→41.51 Å / Num. obs: 64262 / % possible obs: 99.6 % / Redundancy: 3.8 % / Net I/σ(I): 20.67
Reflection shellResolution: 2.38→2.42 Å

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementResolution: 2.382→41.506 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2608 3272 5.09 %
Rwork0.2023 --
Obs0.2052 64262 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.382→41.506 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9949 443 2 6 10400
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910655
X-RAY DIFFRACTIONf_angle_d1.38814422
X-RAY DIFFRACTIONf_dihedral_angle_d18.3014098
X-RAY DIFFRACTIONf_chiral_restr0.1061551
X-RAY DIFFRACTIONf_plane_restr0.0051762
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.3823-2.41790.34671330.30372554X-RAY DIFFRACTION95
2.4179-2.45570.34861360.29062655X-RAY DIFFRACTION98
2.4557-2.49590.34261280.29662602X-RAY DIFFRACTION97
2.4959-2.53890.32841500.2732617X-RAY DIFFRACTION97
2.5389-2.58510.34451430.2762601X-RAY DIFFRACTION96
2.5851-2.63480.27231360.2572619X-RAY DIFFRACTION98
2.6348-2.68860.29571620.25352655X-RAY DIFFRACTION98
2.6886-2.7470.30791440.25172643X-RAY DIFFRACTION98
2.747-2.81090.29051230.23422671X-RAY DIFFRACTION98
2.8109-2.88120.3321490.2482645X-RAY DIFFRACTION99
2.8812-2.95910.29881360.24512654X-RAY DIFFRACTION98
2.9591-3.04610.29681200.23442651X-RAY DIFFRACTION98
3.0461-3.14440.31491560.23062577X-RAY DIFFRACTION96
3.1444-3.25680.30721430.23032640X-RAY DIFFRACTION98
3.2568-3.38710.27651590.22382673X-RAY DIFFRACTION99
3.3871-3.54120.2811580.21152645X-RAY DIFFRACTION99
3.5412-3.72780.27211350.21142714X-RAY DIFFRACTION99
3.7278-3.96120.26281530.18992666X-RAY DIFFRACTION99
3.9612-4.26670.23271490.18012613X-RAY DIFFRACTION96
4.2667-4.69560.2151390.16332721X-RAY DIFFRACTION99
4.6956-5.37380.23491380.16852692X-RAY DIFFRACTION99
5.3738-6.76560.23441420.19762717X-RAY DIFFRACTION98
6.7656-41.51180.21551400.16612765X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 45.0357 Å / Origin y: 0.6252 Å / Origin z: 26.7772 Å
111213212223313233
T0.4407 Å2-0.0551 Å20.0099 Å2-0.4454 Å2-0.0727 Å2--0.3955 Å2
L0.7168 °2-0.2261 °2-0.6608 °2-0.821 °20.4031 °2--2.113 °2
S-0.0772 Å °-0.3169 Å °-0.0778 Å °0.1007 Å °0.2385 Å °-0.101 Å °0.2242 Å °0.4145 Å °-0.1414 Å °
Refinement TLS groupSelection details: all

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