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- PDB-6wxq: Crystal structure of CRISPR-associated transcription factor Csa3 ... -

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Basic information

Entry
Database: PDB / ID: 6wxq
TitleCrystal structure of CRISPR-associated transcription factor Csa3 complexed with cA4
Components
  • CRISPR-associated transcription factor Csa3 (Type I-A)
  • cyclic tetraadenylate
KeywordsTRANSCRIPTION / CARF domain / wHTH / ring nuclease / second messenger
Function / homology
Function and homology information


Rossmann fold - #11700 / CRISPR locus-related putative DNA-binding protein Csa3 / Csa3 CRISPR-associated Rossmann-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Rossmann fold - #11700 / CRISPR locus-related putative DNA-binding protein Csa3 / Csa3 CRISPR-associated Rossmann-like domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / CRISPR-associated protein Csa5 (Type I-A)
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsXia, P. / Dutta, A. / Parashar, V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119504 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Structural basis of cyclic oligoadenylate binding to the transcription factor Csa3 outlines cross talk between type III and type I CRISPR systems.
Authors: Xia, P. / Dutta, A. / Gupta, K. / Batish, M. / Parashar, V.
History
DepositionMay 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Oct 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

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Assembly

Deposited unit
B: CRISPR-associated transcription factor Csa3 (Type I-A)
A: CRISPR-associated transcription factor Csa3 (Type I-A)
E: cyclic tetraadenylate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9387
Polymers57,5703
Non-polymers3684
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint-31 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.793, 118.830, 64.046
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-439-

HOH

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Components

#1: Protein CRISPR-associated transcription factor Csa3 (Type I-A) / Csa3


Mass: 28148.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Gene: SSOP1_1568 / Plasmid: pBB75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A157T189
#2: RNA chain cyclic tetraadenylate


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 51.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1 M potassium sulfate, 0.1 M sodium potassium phosphate, pH 5.8, 16% PEG3350

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Data collection

DiffractionMean temperature: 93.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 17, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 36695 / % possible obs: 100 % / Redundancy: 8 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.034 / Rrim(I) all: 0.098 / Χ2: 1.017 / Net I/σ(I): 9.5 / Num. measured all: 293709
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.097.40.37118100.9240.1440.3991.02399.9
2.09-2.127.50.32817860.940.1270.3531.03100
2.12-2.167.40.28817870.9550.1120.3091.043100
2.16-2.217.20.28418520.9470.1110.3061.05499.9
2.21-2.266.90.25817800.9530.1050.2791.04799.9
2.26-2.317.10.22918070.9650.0910.2471.03100
2.31-2.377.80.20818000.9750.0780.2231.01100
2.37-2.437.50.18718330.9810.0720.21.00799.9
2.43-2.57.60.17218100.9820.0660.1851.021100
2.5-2.588.50.16318200.9850.0590.1731.00799.9
2.58-2.688.50.14618230.9870.0530.1551.025100
2.68-2.788.60.13518180.9910.0480.1430.985100
2.78-2.918.60.1218360.9920.0430.1280.98599.9
2.91-3.068.70.10518270.9940.0370.1111.029100
3.06-3.258.60.09418320.9950.0340.11.05100
3.25-3.518.60.08118410.9950.0290.0870.999100
3.51-3.868.30.07518500.9960.0270.081.029100
3.86-4.427.60.06218820.9970.0240.0661.034100
4.42-5.568.50.05618840.9980.020.061.006100
5.56-509.10.04520170.9990.0160.0480.96199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.86 Å39.61 Å
Translation4.86 Å39.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
SCALEPACKdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2WTE

2wte


Resolution: 2.05→37.64 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 18.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2052 1827 5 %
Rwork0.16 34699 -
obs0.1622 36526 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85 Å2 / Biso mean: 30.8537 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 2.05→37.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 112 284 3711
Biso mean--27.47 36.45 -
Num. residues----419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.110.22061360.17312594273099
2.11-2.170.21131390.163426292768100
2.17-2.240.22041400.160526532793100
2.24-2.320.19141370.158426142751100
2.32-2.410.18731390.151726432782100
2.41-2.520.21571390.167926352774100
2.52-2.650.20831410.170326772818100
2.65-2.820.23231380.177526342772100
2.82-3.040.22291400.180326612801100
3.04-3.340.22491410.170826802821100
3.34-3.820.19721430.161126962839100
3.82-4.820.18331420.12727222864100
4.82-37.640.19731520.162128613013100
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)
12.3390.7431-0.78461.7642-0.29763.3609-0.0415-0.0775-0.55610.00420.0001-0.18640.11570.07110.03650.1895-0.0059-0.01620.10820.01150.3058-21.67913.556-25.156
21.4742-0.22770.56661.97340.58910.71450.042-0.2012-0.76110.096-0.07160.04660.241-0.11430.04020.2904-0.0424-0.04810.11410.08710.4623-28.3276.207-20.335
32.3324-0.79580.24244.60060.68952.9254-0.1572-0.5124-0.65230.19310.0873-0.04230.45590.2760.02710.2203-0.0532-0.03690.21490.07120.3484-25.67910.952-14.851
45.8241-3.2956-2.14284.59241.41784.1767-0.2089-1.0214-0.0050.54540.1602-0.04020.39820.0380.04080.2774-0.0596-0.05410.40540.04260.1467-26.30221.276-6.505
52.5808-0.14410.551.46450.25790.9097-0.0416-0.3599-0.26430.17690.04110.0166-0.0923-0.0818-0.01010.1683-0.0261-0.01030.15290.03890.1062-26.16122.265-17.523
63.81510.79431.53242.17770.48613.80240.04030.0654-0.0179-0.0027-0.0527-0.0813-0.09750.11080.0220.1151-0.00770.00180.1183-0.0010.1547-24.33724.605-25.478
72.50671.42681.2515.17111.62842.05150.058-0.18690.03740.1917-0.0608-0.2269-0.31010.13270.05350.1655-0.0244-0.00960.1611-0.00480.1213-20.00433.269-22.433
83.2803-0.0792-0.31622.8882-0.98874.72780.2069-0.46280.49860.8147-0.1515-0.0582-0.22310.0109-0.06320.3406-0.059-0.00790.1805-0.06520.2603-15.38651.409-23.42
95.464.31731.66144.4132.12492.91890.1377-0.16510.90390.0665-0.2861-0.1874-0.15730.07410.06930.246-0.0220.01720.1590.0310.4706-7.78556.784-31.462
103.39641.93160.34285.76880.251.62250.0799-0.05440.41350.11270.0337-0.6322-0.20060.3274-0.0830.1922-0.0209-0.00270.236-0.01450.2764-4.3146.196-26.636
115.03311.3045-1.01473.1018-2.24022.3350.14080.34070.1501-0.1424-0.1562-0.2198-0.2365-0.1338-0.0040.1905-0.0161-0.00290.1160.01220.1623-15.63645.425-31.641
123.3162-0.38740.84520.78110.25891.3569-0.0768-0.14840.26290.0935-0.04010.1242-0.098-0.11130.09510.1631-0.0032-0.00190.1326-0.02030.1813-47.65135.338-26.646
133.0769-0.1211-0.38841.7140.65582.50570.0548-0.28890.16040.1572-0.10370.0961-0.0028-0.07960.02520.1332-0.00680.00690.1744-0.02170.1041-35.59834.477-20.546
140.55610.05741.73260.67490.80885.58840.086-0.10360.07520.26920.0355-0.2008-0.1831-0.1091-0.11860.3763-0.0258-0.02870.3885-0.02510.2329-25.83234.9695.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 1:28 )B1 - 28
2X-RAY DIFFRACTION2( CHAIN B AND RESID 29:55 )B29 - 55
3X-RAY DIFFRACTION3( CHAIN B AND RESID 56:70 )B56 - 70
4X-RAY DIFFRACTION4( CHAIN B AND RESID 71:84 )B71 - 84
5X-RAY DIFFRACTION5( CHAIN B AND RESID 85:110 )B85 - 110
6X-RAY DIFFRACTION6( CHAIN B AND RESID 111:127 )B111 - 127
7X-RAY DIFFRACTION7( CHAIN B AND RESID 128:140 )B128 - 140
8X-RAY DIFFRACTION8( CHAIN B AND RESID 141:157 )B141 - 157
9X-RAY DIFFRACTION9( CHAIN B AND RESID 158:172 )B158 - 172
10X-RAY DIFFRACTION10( CHAIN B AND RESID 173:186 )B173 - 186
11X-RAY DIFFRACTION11( CHAIN B AND RESID 187:211 )B187 - 211
12X-RAY DIFFRACTION12( CHAIN A AND RESID 1:70 )A1 - 70
13X-RAY DIFFRACTION13( CHAIN A AND RESID 71:127 )A71 - 127
14X-RAY DIFFRACTION14( CHAIN A AND RESID 128:212 )A128 - 212

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