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- PDB-6aay: the Cas13b binary complex -

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Basic information

Entry
Database: PDB / ID: 6aay
Titlethe Cas13b binary complex
Components
  • Bergeyella zoohelcum Cas13b (R1177A) mutant
  • RNA (52-MER)
KeywordsRNA BINDING PROTEIN/RNA / Cas13b / CRISPR / crRNA / Cas / binary complex / RNA BINDING PROTEIN-RNA complex
Function / homologyRNA / RNA (> 10) / Cyclic nucleotide-binding domain-containing protein
Function and homology information
Biological speciesBergeyella zoohelcum ATCC 43767 (bacteria)
Bergeyella zoohelcum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 Å
AuthorsBo, Z. / Weiwei, Y. / Yangmiao, Y. / Ouyang, S.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31770948 China
CitationJournal: Cell Res. / Year: 2018
Title: Structural insights into Cas13b-guided CRISPR RNA maturation and recognition.
Authors: Zhang, B. / Ye, W.W. / Ye, Y.M. / Zhou, H. / Saeed, A.F.U.H. / Chen, J. / Lin, J.Y. / Perculija, V. / Chen, Q. / Chen, C.J. / Chang, M.X. / Choudhary, M.I. / Ouyang, S.Y.
History
DepositionJul 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bergeyella zoohelcum Cas13b (R1177A) mutant
B: RNA (52-MER)


Theoretical massNumber of molelcules
Total (without water)166,6612
Polymers166,6612
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-60 kcal/mol
Surface area64630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.740, 196.740, 96.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Bergeyella zoohelcum Cas13b (R1177A) mutant


Mass: 147588.750 Da / Num. of mol.: 1 / Mutation: R1177A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bergeyella zoohelcum ATCC 43767 (bacteria)
Gene: HMPREF9699_02005 / Production host: Escherichia coli (E. coli) / References: UniProt: K1LVU1
#2: RNA chain RNA (52-MER)


Mass: 19072.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Bergeyella zoohelcum (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.15 M Sodium chloride, 0.1 M Sodium citrate (pH 5.5), 22% (w/v) Polyethylene glycol 1,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→65.58 Å / Num. obs: 47521 / % possible obs: 99.88 % / Redundancy: 20 % / Biso Wilson estimate: 50.315 Å2 / CC1/2: 0.997 / Net I/σ(I): 12.2
Reflection shellResolution: 2.79→2.89 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2376 / CC1/2: 0.544 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→65.02 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.873 / SU ML: 0.32 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27613 2390 5 %RANDOM
Rwork0.22115 ---
obs0.22393 45072 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.35 Å2
Refinement stepCycle: 1 / Resolution: 2.79→65.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10107 1118 0 37 11262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01411559
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710051
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.62215763
X-RAY DIFFRACTIONr_angle_other_deg1.011.72923694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56651195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17723.88598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.827152056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2251551
X-RAY DIFFRACTIONr_chiral_restr0.0750.21492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211923
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6016.94792
X-RAY DIFFRACTIONr_mcbond_other4.66.8994791
X-RAY DIFFRACTIONr_mcangle_it7.14710.3485983
X-RAY DIFFRACTIONr_mcangle_other7.14610.355984
X-RAY DIFFRACTIONr_scbond_it5.2477.386766
X-RAY DIFFRACTIONr_scbond_other5.2477.386767
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.21910.9029780
X-RAY DIFFRACTIONr_long_range_B_refined12.42179.68213789
X-RAY DIFFRACTIONr_long_range_B_other12.42179.67913790
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.79→2.862 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 162 -
Rwork0.331 3297 -
obs--100 %

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