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- PDB-6dtd: High-resolution crystal structure of Cas13b from Prevotella buccae -

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Basic information

Entry
Database: PDB / ID: 6dtd
TitleHigh-resolution crystal structure of Cas13b from Prevotella buccae
Components
  • RNA (37-MER)
  • nuclease
KeywordsHYDROLASE/RNA / Nuclease / HYDROLASE-RNA complex
Function / homologyCITRIC ACID / RNA / RNA (> 10) / Uncharacterized protein
Function and homology information
Biological speciesPrevotella buccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsSlaymaker, I.M.S. / Zhang, F.Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 MH110049-02 United States
CitationJournal: Cell Rep / Year: 2019
Title: High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage.
Authors: Slaymaker, I.M. / Mesa, P. / Kellner, M.J. / Kannan, S. / Brignole, E. / Koob, J. / Feliciano, P.R. / Stella, S. / Abudayyeh, O.O. / Gootenberg, J.S. / Strecker, J. / Montoya, G. / Zhang, F.
History
DepositionJun 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 21, 2020Group: Data collection / Derived calculations
Category: pdbx_struct_conn_angle / reflns_shell / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id ..._pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _reflns_shell.Rmerge_I_obs / _reflns_shell.pdbx_Rrim_I_all / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: nuclease
C: RNA (37-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,28917
Polymers146,0502
Non-polymers2,23915
Water15,601866
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-89 kcal/mol
Surface area48140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.821, 124.646, 140.728
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / RNA chain , 2 types, 2 molecules AC

#1: Protein nuclease /


Mass: 134285.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prevotella buccae (bacteria) / Gene: HMPREF6485_0083 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: E6K398, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (37-MER)


Mass: 11763.968 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Prevotella buccae (bacteria)

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Non-polymers , 5 types, 881 molecules

#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 866 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: salt, PEG

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.34→46.654 Å / Num. obs: 209453 / % possible obs: 80.5 % / Redundancy: 10.782 % / Biso Wilson estimate: 36.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.132 / Χ2: 1.036 / Net I/σ(I): 7.57 / Num. measured all: 3076708 / Scaling rejects: 240
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obs% possible allRmerge(I) obsMean I/σ(I) obsRrim(I) allCC1/2
1.34-1.381.35424649.5
1.38-1.412.559740829.2
1.41-1.463.5921208048.9
1.46-1.54.3261631468
1.5-1.555.2991870780.58.3690.19.304
1.55-1.66.5712031990.35.2790.245.737
1.6-1.668.3832126397.93.6810.443.9250.147
1.66-1.7311.408209371002.580.822.7020.317
1.73-1.8113.821200861001.6961.521.7610.618
1.81-1.914.156192461001.1172.51.1590.801
1.9-213.923182581000.7074.060.7340.914
2-2.1213.5173481000.4496.290.4670.963
2.12-2.2713.719163091000.2849.790.2950.984
2.27-2.4514.325152161000.19913.660.2060.992
2.45-2.6814.03140201000.1517.310.1560.994
2.68-313.355127071000.11221.750.1160.996
3-3.4713.62112771000.08927.180.0930.996
3.47-4.2414.1295961000.07831.280.0810.997
4.24-613.23575151000.07331.750.0760.997
6-46.65412.94142961000.07131.750.0740.997

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
AutoSolphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.65→46.654 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.16
RfactorNum. reflection% reflection
Rfree0.185 9752 5 %
Rwork0.1532 --
obs0.1548 191464 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.21 Å2 / Biso mean: 46.6399 Å2 / Biso min: 21.83 Å2
Refinement stepCycle: final / Resolution: 1.65→46.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8486 780 246 866 10378
Biso mean--88.41 47.95 -
Num. residues----1090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.66880.38015790.3484109011148093
1.6688-1.68840.34646180.3167116301224899
1.6884-1.7090.33666190.3126117291234899
1.709-1.73060.31186140.29141166312277100
1.7306-1.75340.29356210.26411180312424100
1.7534-1.77740.31866160.2661172212338100
1.7774-1.80280.29586240.25251175912383100
1.8028-1.82970.28856150.24291173312348100
1.8297-1.85830.27746230.2381179312416100
1.8583-1.88880.24936250.21541174012365100
1.8888-1.92130.24226150.20051176212377100
1.9213-1.95630.21016190.17811173312352100
1.9563-1.99390.20096180.16861176712385100
1.9939-2.03460.20016210.16311173012351100
2.0346-2.07880.1966230.15381177912402100
2.0788-2.12720.18866170.14531176612383100
2.1272-2.18040.19626180.14341173812356100
2.1804-2.23940.16926200.13881176512385100
2.2394-2.30520.17126130.13241178212395100
2.3052-2.37960.17886160.13241177212388100
2.3796-2.46470.18146220.13571173912361100
2.4647-2.56340.18266160.13771175812374100
2.5634-2.680.17996200.13941174212362100
2.68-2.82130.19856130.15021180412417100
2.8213-2.9980.17876200.14841173212352100
2.998-3.22950.1776120.14941178412396100
3.2295-3.55440.17786180.14291175512373100
3.5544-4.06840.16396220.12481176012382100
4.0684-5.12480.12896160.11891177012386100
5.1248-46.67270.19156240.17561172712351100

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