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- PDB-6w11: The structure of Sulfolobus solfataricus Csa3 in complex with cyc... -

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Basic information

Entry
Database: PDB / ID: 6w11
TitleThe structure of Sulfolobus solfataricus Csa3 in complex with cyclic tetraadenylate (cA4)
Components
  • CRISPR locus-related putative DNA-binding protein Csa3
  • cA4
KeywordsTRANSCRIPTION / CARF / CRISPR-Cas / cyclic oligoadenylate / cA4
Function / homologyCRISPR locus-related putative DNA-binding protein Csa3 / defense response to virus / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / RNA / CRISPR locus-related putative DNA-binding protein Csa3
Function and homology information
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsCharbonneau, A.A. / Gauvin, C.C. / Lawrence, C.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1413534 United States
CitationJournal: Biomolecules / Year: 2021
Title: Cyclic Tetra-Adenylate (cA 4 ) Recognition by Csa3; Implications for an Integrated Class 1 CRISPR-Cas Immune Response in Saccharolobus solfataricus.
Authors: Charbonneau, A.A. / Eckert, D.M. / Gauvin, C.C. / Lintner, N.G. / Lawrence, C.M.
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: CRISPR locus-related putative DNA-binding protein Csa3
A: CRISPR locus-related putative DNA-binding protein Csa3
C: cA4


Theoretical massNumber of molelcules
Total (without water)49,4153
Polymers49,4153
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-29 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.094, 93.369, 105.191
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CRISPR locus-related putative DNA-binding protein Csa3


Mass: 24071.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: csa3, SSO1445 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q97Y88
#2: RNA chain cA4


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Cyclic 4 base RNA / Source: (synth.) Saccharolobus solfataricus (archaea)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.35 Å3/Da / Density % sol: 47.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 14-22% PEG MME 550, 100mM imidazole, 150mM malate, 10mM cA4

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Data collection

DiffractionMean temperature: 160 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 16551 / % possible obs: 96.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.026 / Rrim(I) all: 0.084 / Χ2: 2.153 / Net I/σ(I): 23.9 / Num. measured all: 171587
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.4910.40.828240.7370.2650.8630.801100
2.49-2.5410.70.6398480.8970.2030.6710.806100
2.54-2.5910.60.6178320.9220.2020.650.859100
2.59-2.6410.60.4838300.9480.1550.5080.906100
2.64-2.710.80.4098450.9590.130.4290.944100
2.7-2.7610.80.3728260.9660.1170.390.926100
2.76-2.8310.80.2858480.9790.090.2990.901100
2.83-2.910.80.2318530.9880.0730.2420.976100
2.9-2.9910.90.1998270.9910.0630.2091.057100
2.99-3.0910.80.1498510.9940.0470.1562.488100
3.09-3.210.90.138410.9940.0410.1371.231100
3.2-3.3210.80.1128560.9950.0350.1181.484100
3.32-3.4810.70.1198480.9950.0380.1252.517100
3.48-3.668.20.1546500.7250.0590.1663.75978
3.66-3.897.20.1517430.9640.0580.1635.87484.3
3.89-4.199.90.076580.9970.0230.0743.4276.2
4.19-4.6110.70.0638610.9970.020.0664.33199.9
4.61-5.2810.70.0578730.9980.0180.063.76499.7
5.28-6.6510.50.069040.9980.0190.0634.023100
6.65-509.70.0499330.9980.0170.0524.40897.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WTE

2wte


Resolution: 2.46→27.91 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.56
RfactorNum. reflection% reflection
Rfree0.2428 1648 10.01 %
Rwork0.2027 --
obs0.2067 16462 95.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 186.04 Å2 / Biso mean: 85.6564 Å2 / Biso min: 36.12 Å2
Refinement stepCycle: final / Resolution: 2.46→27.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 88 0 21 3398
Biso mean---68.81 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.46-2.530.34641280.28771161128992
2.53-2.610.3491410.268612601401100
2.61-2.710.3191410.257812651406100
2.71-2.810.32781390.272712581397100
2.81-2.940.29131410.259812651406100
2.94-3.10.35531420.257912791421100
3.1-3.290.29431430.250612841427100
3.29-3.540.30671390.23671259139899
3.54-3.90.29521140.25271008112278
3.9-4.460.18031190.17181067118683
4.46-5.610.18961460.159613151461100
5.62-27.910.19861550.161913931548100
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)
14.9111-0.9259-0.25643.35620.2955.45180.02510.28190.0265-0.18640.1083-0.3961-0.01150.5506-0.12630.4345-0.05980.06580.465-0.08720.4754-8.4764-9.25741.7322
26.7341-5.7054-3.56268.29691.71035.61260.06110.00971.6936-0.0105-0.32361.4672-0.8495-0.57470.23860.70210.00850.09280.4776-0.17391.2044-24.56978.10458.366
34.38725.8633.10078.24312.59988.2403-1.5037-1.26651.9224-1.24580.20631.9798-0.8013-0.71451.10351.30420.4377-0.13061.3126-0.04062.0824-36.283529.18477.305
46.846-4.25834.72615.6309-5.69445.78110.57020.57840.5389-0.6445-0.25651.4038-0.01230.7523-0.52041.0474-0.02420.04960.7013-0.0611.3439-29.855416.1656.5544
55.7719-3.1999-2.38428.5606-0.44136.23150.4273-1.9720.30181.4612-0.1344-0.23970.25340.5906-0.20080.7861-0.24750.14041.0654-0.10960.6477-27.0743-16.185125.4038
68.22831.72833.48924.5426-0.29797.13390.6388-0.9986-0.3836-0.1806-0.28180.55360.5181-0.6349-0.28380.5894-0.13820.11270.7466-0.16490.6452-35.5404-19.357918.6632
73.71140.7758-1.65979.4934-3.72296.82970.0295-0.56010.6462-0.14930.00050.7079-0.1786-0.1801-0.19120.5888-0.01650.080.6905-0.29230.6635-34.1261-6.125516.7047
83.7124-3.0529-0.52899.56271.45682.59690.2665-1.40360.42180.4939-0.12330.54190.1454-0.6231-0.07030.6962-0.11680.09010.8292-0.24840.4672-25.4625-8.858721.3197
97.71442.94582.61285.78680.18636.97030.3768-1.09820.44230.7007-0.5636-0.0928-0.00840.20320.11460.539-0.15780.07420.5119-0.07050.4348-20.681-7.796317.7131
106.08044.93536.12174.05175.05419.2331-0.1222-0.49860.7969-0.3675-0.22950.243-0.74420.31650.32750.7992-0.16610.16190.915-0.27910.6987-5.48096.272923.8354
118.45730.82010.11198.939-0.70634.6032-0.0461.33010.04730.18570.1084-0.9203-0.23021.3258-0.13140.9714-0.1428-0.0281.0907-0.18330.62510.571412.347135.9429
122.6693-0.6837-3.07277.4634-0.96598.4141-0.3541-0.4188-1.89850.63550.1533-0.72080.55841.74080.42530.961-0.0014-0.14071.2481-0.220.6932-1.32972.312429.0825
134.9545-4.6372-6.88145.20616.65659.9379-1.07240.3287-1.86930.12040.27560.27561.15490.33460.60340.8146-0.11650.01960.6626-0.01580.7034-21.0677-19.90917.4941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 110 )B1 - 110
2X-RAY DIFFRACTION2chain 'B' and (resid 111 through 157 )B111 - 157
3X-RAY DIFFRACTION3chain 'B' and (resid 158 through 177 )B158 - 177
4X-RAY DIFFRACTION4chain 'B' and (resid 178 through 212 )B178 - 212
5X-RAY DIFFRACTION5chain 'A' and (resid 1 through 28 )A1 - 28
6X-RAY DIFFRACTION6chain 'A' and (resid 29 through 55 )A29 - 55
7X-RAY DIFFRACTION7chain 'A' and (resid 56 through 84 )A56 - 84
8X-RAY DIFFRACTION8chain 'A' and (resid 85 through 97 )A85 - 97
9X-RAY DIFFRACTION9chain 'A' and (resid 98 through 127 )A98 - 127
10X-RAY DIFFRACTION10chain 'A' and (resid 128 through 157 )A128 - 157
11X-RAY DIFFRACTION11chain 'A' and (resid 158 through 185 )A158 - 185
12X-RAY DIFFRACTION12chain 'A' and (resid 186 through 212 )A186 - 212
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 4 )C1 - 4

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