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- PDB-6ae2: Crystal structure of Csm3 of the type III-A CRISPR-Cas effector c... -

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Basic information

Entry
Database: PDB / ID: 6ae2
TitleCrystal structure of Csm3 of the type III-A CRISPR-Cas effector complex
ComponentsCsm3
KeywordsRNA BINDING PROTEIN / CRISPR-Cas / Cas protein / crRNA / Csm complex
Function / homologyCRISPR-associated RAMP Csm3 / CRISPR type III-associated protein / RAMP superfamily / endonuclease activity / defense response to virus / CRISPR system Cms endoribonuclease Csm3
Function and homology information
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.701 Å
AuthorsNumata, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04759 Japan
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.
Authors: Takeshita, D. / Sato, M. / Inanaga, H. / Numata, T.
History
DepositionAug 3, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 27, 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: Csm3
B: Csm3


Theoretical massNumber of molelcules
Total (without water)55,4772
Polymers55,4772
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-7 kcal/mol
Surface area17890 Å2
Unit cell
Length a, b, c (Å)78.331, 78.331, 182.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Csm3


Mass: 27738.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1) (archaea)
Strain: ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1
Gene: TVG0114661 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97CJ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 180 mM di-ammonium tartrate, 18% (w/v) PEG 3350, 3% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16335 / % possible obs: 99.7 % / Redundancy: 13.9 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.08 / Χ2: 3.23 / Net I/σ(I): 18.8 / Num. measured all: 227320
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.7-2.7514.20.4667672.9861100
2.75-2.8140.448122.9721100
2.8-2.8514.10.3757892.9341100
2.85-2.91140.3298083.0281100
2.91-2.9714.20.2437823.0631100
2.97-3.0414.20.2147993.1041100
3.04-3.1214.20.1858053.11100
3.12-3.214.20.1597983.0441100
3.2-3.314.20.1318243.0621100
3.3-3.414.30.1168033.0511100
3.4-3.5214.30.1077953.0981100
3.52-3.6614.30.0858193.0151100
3.66-3.8314.20.0688113.09199.9
3.83-4.0314.20.0588103.051100
4.03-4.29140.0538323.1661100
4.29-4.6213.80.0478353.1851100
4.62-5.0813.90.0428202.947199.9
5.08-5.8113.80.0468443.2021100
5.81-7.3213.30.0458723.432199.9
7.32-5011.40.0419106.399195.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å39.46 Å
Translation3 Å39.46 Å

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Processing

Software
NameVersionClassification
HKL-2000data scaling
MOLREP10.2.31phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→39.455 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.56
RfactorNum. reflection% reflection
Rfree0.2428 823 5.06 %
Rwork0.2111 --
obs0.2128 16271 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 168.53 Å2 / Biso mean: 49.6898 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: final / Resolution: 2.701→39.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 0 6 2867
Biso mean---30.02 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022900
X-RAY DIFFRACTIONf_angle_d0.5923881
X-RAY DIFFRACTIONf_chiral_restr0.046431
X-RAY DIFFRACTIONf_plane_restr0.002487
X-RAY DIFFRACTIONf_dihedral_angle_d3.1641764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.701-2.87010.30351460.251924822628100
2.8701-3.09170.27651230.236425372660100
3.0917-3.40260.28121440.231725392683100
3.4026-3.89460.23331420.204125562698100
3.8946-4.90530.20461310.173225992730100
4.9053-39.4590.23421370.22372735287299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.71880.0373-0.03280.89580.69873.10310.04880.10710.10360.213-0.08430.0199-0.02840.00270.02530.15340.0185-0.00420.1949-0.07770.166315.637845.204156.5587
23.0232-0.68820.19912.1819-0.01442.49640.2157-0.2419-0.06240.167-0.0371-0.29960.29740.3975-0.05310.19040.0171-0.07740.3469-0.07750.205922.570140.3167160.215
38.507-2.42793.50468.03111.78513.3726-0.96960.74550.07670.07730.81760.4758-0.8892-0.80530.35040.78410.20330.13591.1654-0.05430.4752.136250.8629147.4786
41.47010.37720.26331.78431.11873.13380.27620.1536-0.10720.12160.017-0.02840.32610.3667-0.0150.1383-0.00620.01660.2631-0.04190.220820.835442.7444153.4671
51.77770.48760.15510.6881.00182.998-0.12570.07830.4256-0.03070.1362-0.0847-0.26940.09880.17530.33930.0798-0.1110.2127-0.10360.283113.245735.4203133.6282
61.22110.6361-0.15452.8735-0.55851.7983-0.2168-0.423-0.1410.05740.2551-0.14340.703-0.0847-0.19150.49210.2591-0.07310.3517-0.05350.207619.166518.366138.6653
71.6631-0.1265-1.43445.96710.85732.6745-0.91961.09861.9912-0.83080.2254-0.0097-2.3806-0.52650.33521.32110.0403-0.13180.58230.15770.71729.687945.2182124.0705
82.04580.37910.67071.71720.97093.64610.0221-0.3082-0.0543-0.00380.2374-0.2230.33660.1573-0.09690.23770.1058-0.01690.2284-0.06230.235517.817426.5635131.0607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 5:47)A5 - 47
2X-RAY DIFFRACTION2(chain A and resid 48:112)A48 - 112
3X-RAY DIFFRACTION3(chain A and resid 113:124)A113 - 124
4X-RAY DIFFRACTION4(chain A and resid 125:216)A125 - 216
5X-RAY DIFFRACTION5(chain B and resid 5:59)B5 - 59
6X-RAY DIFFRACTION6(chain B and resid 60:112)B60 - 112
7X-RAY DIFFRACTION7(chain B and resid 113:126)B113 - 126
8X-RAY DIFFRACTION8(chain B and resid 127:216)B127 - 216

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