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- PDB-7d3j: Crystal structure of the Cas12i1 R-loop complex after target DNA ... -

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Basic information

Entry
Database: PDB / ID: 7d3j
TitleCrystal structure of the Cas12i1 R-loop complex after target DNA cleavage
Components
  • 12i1-WT
  • DNA (23-MER)
  • DNA (28-MER)
  • RNA (43-MER)
KeywordsRNA BINDING PROTEIN / The RNP Complex 2
Function / homologyCITRIC ACID / DNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesLachnospiraceae bacterium ND2006 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, B. / Luo, D.Y. / Li, Y. / OuYang, S.Y.
CitationJournal: Nat Commun / Year: 2021
Title: Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1.
Authors: Zhang, B. / Luo, D. / Li, Y. / Perculija, V. / Chen, J. / Lin, J. / Ye, Y. / Ouyang, S.
History
DepositionSep 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 30, 2021Group: Source and taxonomy / Category: entity_src_gen / pdbx_entity_src_syn
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Nov 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: 12i1-WT
B: RNA (43-MER)
C: DNA (28-MER)
D: DNA (23-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,5085
Polymers165,3164
Non-polymers1921
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17410 Å2
ΔGint-103 kcal/mol
Surface area59830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.801, 141.974, 208.296
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (28-MER)


Mass: 12326.935 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)
#4: DNA chain DNA (23-MER)


Mass: 12257.882 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Lachnospiraceae bacterium ND2006 (bacteria)

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Protein / RNA chain , 2 types, 2 molecules AB

#1: Protein 12i1-WT


Mass: 126950.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli)
#2: RNA chain RNA (43-MER)


Mass: 13781.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachnospiraceae bacterium ND2006 (bacteria)
Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 41 molecules

#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium citrate (pH 5.4), 15% (w/v) Polyethylene glycol 3350, 0.2 M lithium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→58.73 Å / Num. obs: 70800 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.6
Reflection shellResolution: 2.45→2.51 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4504 / CC1/2: 0.901

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
Aimless0.7.1data scaling
PHENIX1.13-2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D2L

7d2l


Resolution: 2.45→58.73 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.219 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 3545 5 %RANDOM
Rwork0.2201 ---
obs0.222 67181 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 192.13 Å2 / Biso mean: 61.968 Å2 / Biso min: 25.95 Å2
Baniso -1Baniso -2Baniso -3
1-2.14 Å20 Å20 Å2
2---1.28 Å20 Å2
3----0.87 Å2
Refinement stepCycle: final / Resolution: 2.45→58.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8717 1957 13 40 10727
Biso mean--66.46 43.25 -
Num. residues----1171
LS refinement shellResolution: 2.45→2.514 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 254 -
Rwork0.32 4912 -
all-5166 -
obs--99.85 %

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