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- PDB-6iv8: the selenomethionine(SeMet)-derived Cas13d binary complex -

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Basic information

Entry
Database: PDB / ID: 6iv8
Titlethe selenomethionine(SeMet)-derived Cas13d binary complex
Components
  • RNA (51-MER)
  • RNA (53-MER)
  • The selenomethionine (SeMet)-labeled Cas13d
KeywordsRNA BINDING PROTEIN/RNA / CRISPR / Cas13d / crRNA / binary complex / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10) / TerB_C domain-containing protein
Function and homology information
Biological speciesuncultured Ruminococcus sp (environmental samples)
uncultured Ruminococcus sp. (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsZhang, B. / Ye, Y.M. / Ye, W.W. / OuYang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31770948 China
CitationJournal: Nat Commun / Year: 2019
Title: Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d.
Authors: Zhang, B. / Ye, Y. / Ye, W. / Perculija, V. / Jiang, H. / Chen, Y. / Li, Y. / Chen, J. / Lin, J. / Wang, S. / Chen, Q. / Han, Y.S. / Ouyang, S.
History
DepositionDec 2, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / 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_PubMed / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: The selenomethionine (SeMet)-labeled Cas13d
B: RNA (51-MER)
D: RNA (53-MER)
C: The selenomethionine (SeMet)-labeled Cas13d
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,6916
Polymers250,6424
Non-polymers492
Water11,980665
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.164, 145.733, 249.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A50 - 922
2111C50 - 922
1121B-30 - 20
2121D-30 - 20

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.878919, -0.281457, 0.385076), (0.430062, -0.118493, 0.894989), (-0.206272, 0.952229, 0.22519)23.325621, -76.177223, 86.110283

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Components

#1: Protein The selenomethionine (SeMet)-labeled Cas13d


Mass: 108759.344 Da / Num. of mol.: 2 / Mutation: R288A, R823A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Ruminococcus sp (environmental samples)
Gene: SAMEA3545300_02264 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1C5SD84
#2: RNA chain RNA (51-MER)


Mass: 16244.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Ruminococcus sp. (environmental samples)
Production host: Escherichia coli (E. coli)
#3: RNA chain RNA (53-MER)


Mass: 16879.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured Ruminococcus sp. (environmental samples)
Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 665 / 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: 2.49 Å3/Da / Density % sol: 50.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: (0.5% (w/v) Tryptone, 0.1 M HEPES sodium (pH 7.0), 16% (w/v) Polyethylene glycol 3350)

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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: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→62.92 Å / Num. obs: 129626 / % possible obs: 99.7 % / Redundancy: 13.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.053 / Net I/σ(I): 14.5
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 6409 / CC1/2: 0.939 / Rpim(I) all: 0.337 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→62.92 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.179 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 6600 5.1 %RANDOM
Rwork0.1887 ---
obs0.1898 122927 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 200 Å2 / Biso mean: 47.617 Å2 / Biso min: 11.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å2-0 Å2-0 Å2
2---0.42 Å20 Å2
3---0.62 Å2
Refinement stepCycle: final / Resolution: 2.15→62.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14076 2196 2 665 16939
Biso mean--26.35 37.16 -
Num. residues----1829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01416752
X-RAY DIFFRACTIONr_bond_other_d0.0020.01814275
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.60922978
X-RAY DIFFRACTIONr_angle_other_deg1.1031.78333564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.84551726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62322.976783
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.79152681
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7361586
X-RAY DIFFRACTIONr_chiral_restr0.0920.22262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217050
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023204
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDAuth asym-IDNumberRms dev position (Å)
1A701016.33
2B105411.24
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 512 -
Rwork0.208 8974 -
all-9486 -
obs--99.99 %

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