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- PDB-6ltp: Crystal structure of Cas12i2 binary complex -

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Basic information

Entry
Database: PDB / ID: 6ltp
TitleCrystal structure of Cas12i2 binary complex
Components
  • Cas12i2
  • crRNA (56-mer RNA)
KeywordsHYDROLASE/RNA / CRISPR-Cas / Cas12i2 / Cas12i2 binary complex / HYDROLASE / HYDROLASE-RNA complex
Function / homologyRNA / RNA (> 10)
Function and homology information
Biological speciesunidentified (others)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsHuang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31630015 China
National Natural Science Foundation of China (NSFC)31725008 China
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.
Authors: Huang, X. / Sun, W. / Cheng, Z. / Chen, M. / Li, X. / Wang, J. / Sheng, G. / Gong, W. / Wang, Y.
History
DepositionJan 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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
A: Cas12i2
B: crRNA (56-mer RNA)
H: crRNA (56-mer RNA)
G: Cas12i2


Theoretical massNumber of molelcules
Total (without water)279,0424
Polymers279,0424
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18840 Å2
ΔGint-62 kcal/mol
Surface area93830 Å2
Unit cell
Length a, b, c (Å)146.309, 146.309, 144.602
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 173 or (resid 174...
d_2ens_1(chain "G" and (resid 1 through 61 or (resid 62...
d_1ens_2chain "B"
d_2ens_2chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METGLNA2 - 227
d_12ens_1LYSGLUA229 - 230
d_13ens_1GLNSERA232 - 233
d_14ens_1ASNVALA235 - 240
d_15ens_1ALAGLNA242 - 332
d_16ens_1ASPASPA334
d_17ens_1TYRLYSA336 - 337
d_18ens_1GLNGLNA339 - 492
d_19ens_1GLYTRPA494 - 580
d_110ens_1ALALEUA582 - 737
d_111ens_1ALAGLYA739 - 920
d_21ens_1METTHRE2 - 175
d_22ens_1ASPGLNE178 - 229
d_23ens_1LYSGLUE231 - 232
d_24ens_1GLNSERE234 - 235
d_25ens_1ASNVALE237 - 242
d_26ens_1ALAGLNE244 - 334
d_27ens_1ASPASPE336
d_28ens_1TYRLYSE338 - 339
d_29ens_1GLNGLNE341 - 494
d_210ens_1GLYTRPE496 - 582
d_211ens_1ALALEUE584 - 739
d_212ens_1ALAGLYE742 - 923
d_11ens_2AAB
d_21ens_2AAC

NCS ensembles :
ID
ens_1
ens_2

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Components

#1: Protein Cas12i2


Mass: 121469.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified (others)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: RNA chain crRNA (56-mer RNA)


Mass: 18051.766 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe chains A/G contain the expression tag SER (0).

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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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 289 K / Method: evaporation
Details: 0.027 M HEPES pH 7.5, 4 % PEG20K, 0.146 M Na citrate, 0.073 M Tris pH 8.2, 13.87% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. obs: 41862 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Χ2: 0.844 / Net I/σ(I): 13.3
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2069 / CC1/2: 0.534 / Rpim(I) all: 0.323 / Rrim(I) all: 0.759 / Χ2: 0.797 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LTR

6ltr


Resolution: 3.4→48.71 Å / SU ML: 0.3829 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.2185
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 2151 5.42 %
Rwork0.2074 37532 -
obs0.2086 39683 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.08 Å2
Refinement stepCycle: LAST / Resolution: 3.4→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14592 1778 0 12 16382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006416888
X-RAY DIFFRACTIONf_angle_d1.152923255
X-RAY DIFFRACTIONf_chiral_restr0.06592631
X-RAY DIFFRACTIONf_plane_restr0.00792686
X-RAY DIFFRACTIONf_dihedral_angle_d19.39672988
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.700915608183
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS1.47725929289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.480.3171700.27081123X-RAY DIFFRACTION42.64
3.48-3.570.28311300.26282169X-RAY DIFFRACTION83.48
3.57-3.670.2881350.24422584X-RAY DIFFRACTION97.39
3.67-3.770.26661950.23762555X-RAY DIFFRACTION99.6
3.77-3.890.24891580.22132612X-RAY DIFFRACTION99.86
3.9-4.030.24951430.21822642X-RAY DIFFRACTION100
4.03-4.20.24031550.20642633X-RAY DIFFRACTION99.96
4.2-4.390.23931510.19842606X-RAY DIFFRACTION100
4.39-4.620.20171040.18732692X-RAY DIFFRACTION100
4.62-4.910.21131790.1842619X-RAY DIFFRACTION99.96
4.91-5.280.17111060.1832668X-RAY DIFFRACTION100
5.29-5.820.2071860.21072603X-RAY DIFFRACTION100
5.82-6.650.21731600.20892657X-RAY DIFFRACTION99.96
6.66-8.380.19141160.19742688X-RAY DIFFRACTION100
8.38-48.710.20351630.1822681X-RAY DIFFRACTION99.41

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