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- PDB-8q3z: Crystal structure of cA4-bound Can2 from Thermoanaerobacter brockii -

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Basic information

Entry
Database: PDB / ID: 8q3z
TitleCrystal structure of cA4-bound Can2 from Thermoanaerobacter brockii
Components
  • Cyclic tetraadenosine monophosphate (cA4)
  • DUF1887 family protein
KeywordsDNA BINDING PROTEIN / Can2 / cyclic oligoadenylates / cA4 / CARF / CRISPR ancillary nuclease
Function / homologytRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / metal ion binding / : / : / RNA / DUF1887 family protein
Function and homology information
Biological speciesThermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsJungfer, K. / Sigg, A. / Jinek, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)ERC-CoG-820152European Union
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Substrate selectivity and catalytic activation of the type III CRISPR ancillary nuclease Can2.
Authors: Jungfer, K. / Sigg, A. / Jinek, M.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DUF1887 family protein
B: DUF1887 family protein
X: Cyclic tetraadenosine monophosphate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1835
Polymers104,0733
Non-polymers1102
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-23 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.966, 79.133, 94.214
Angle α, β, γ (deg.)90.000, 95.580, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein DUF1887 family protein


Mass: 51400.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter brockii subsp. finnii Ako-1 (bacteria)
Gene: Thebr_0943 / Production host: Escherichia coli (E. coli) / References: UniProt: E8URK0
#2: RNA chain Cyclic tetraadenosine monophosphate (cA4)


Type: Polycyclic / Class: Antiviral / Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Cyclic oligoadenylates such as c-tetraAMP were found to be novel bacterial second messengers. Antiviral in context of signalling for Type III CRISPR-Cas systems.
Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002431
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
Compound detailsCRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic ...CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages. Cyclic oligoadenylate signaling was found to be essential for the type III system against the jumbo phage.
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: 2.1 Å3/Da / Density % sol: 41.43 % / Description: plate-shaped crystals
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 50 mM Tris pH 8, 17.1% (v/v) PEG 550 MME, 4.3% (w/v) PEG 2000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.15→93.77 Å / Num. obs: 14187 / % possible obs: 95.65 % / Redundancy: 6.3 % / Biso Wilson estimate: 71.69 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.0599 / Rrim(I) all: 0.15 / Net I/σ(I): 7.3
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 2.24 / Num. unique obs: 1474 / CC1/2: 0.708 / Rpim(I) all: 0.3761 / Rrim(I) all: 0.981 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
autoPROC20230726data scaling
XDS20220110data reduction
Coot0.9.8.9model building
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→93.77 Å / SU ML: 0.4865 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7464
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2563 709 5.02 %
Rwork0.2234 13422 -
obs0.225 14131 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.71 Å2
Refinement stepCycle: LAST / Resolution: 3.15→93.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7230 0 90 0 7320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427484
X-RAY DIFFRACTIONf_angle_d0.684410084
X-RAY DIFFRACTIONf_chiral_restr0.04591090
X-RAY DIFFRACTIONf_plane_restr0.00311256
X-RAY DIFFRACTIONf_dihedral_angle_d12.46092806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.40.34021480.31362791X-RAY DIFFRACTION99.97
3.4-3.740.36211180.3052214X-RAY DIFFRACTION79.81
3.74-4.280.28391360.23852765X-RAY DIFFRACTION98.61
4.28-5.390.22161550.19642797X-RAY DIFFRACTION100
5.39-93.770.2111520.18212855X-RAY DIFFRACTION99.6
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)
11.39210676921-0.9276880326020.3046524116573.841662871850.460154443682.049321257380.146493785689-1.11926504534-0.1439749206030.579392416295-0.326719369803-0.4480469244280.1645392123770.615268751472-0.06262891986840.520983862898-0.101421640195-0.09572996877161.363309949790.2593561832660.63212124540226.8968173431-10.123129689550.8781061741
22.204432260990.0113719905735-1.225312439620.390721018635-0.05712265411744.631067875780.147576013986-0.0664207229825-0.0695204028166-0.237038956646-0.171204565915-0.219288229667-0.1635787324410.23945336507-7.2578387887E-50.6800164143810.0550358578190.0949573022380.4446651645190.1218163241630.7042713110131.4289360983-1.585197162167.41639589422
32.215459341890.23683443505-0.5806513104681.98716596103-1.055943161632.030380928680.279956997453-0.4672604437630.202455653768-0.000617840912804-0.2409618577870.142133793735-0.63158616668-0.22728797972-8.80104500235E-90.7190199459680.0619881346498-0.02863310332040.5327484291420.05455287516520.56452092919718.63034956713.5146383569319.204109143
42.777556084080.320136163241-0.2787137279273.0476353688-0.4825281657173.739652814020.144962649016-0.861699171614-0.01663580373330.580763346948-0.08614106828450.441498497955-0.198086189064-0.3034750175-0.000917978778460.574182689297-0.08931164246880.0752003820551.07710006327-0.02568863670580.6083940125133.11910528949-0.54149382107748.7331461828
52.750051780780.2223964902830.03678270461473.743735711282.566980984195.232418713910.0212910245920.493432214099-0.233505059667-0.270931453096-0.106193118998-0.1539297476650.359238597136-0.3819113979950.02250300439530.6072403328440.0510332934153-0.04599452117640.340656685539-0.03229328983190.803770152839-1.27051709012-17.37692488150.604225560952
62.08416483682-0.02168896659090.472563923172.50551652531-0.04552349803462.59345164383-0.125071580611-0.202888127054-0.276183363284-0.007017663385610.08140303829170.2642499909170.2468908723930.32918685932-1.01465316839E-80.633477032440.0371606557954-0.05920099741630.4693584094660.08234747577670.6252533548366.74049140151-16.328067703622.1649339719
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 129 )AA1 - 1291 - 129
22chain 'A' and (resid 130 through 362 )AA130 - 362130 - 362
33chain 'A' and (resid 363 through 437 )AA363 - 437363 - 437
44chain 'B' and (resid 1 through 154 )BB1 - 1541 - 154
55chain 'B' and (resid 155 through 317 )BB155 - 317155 - 317
66chain 'B' and (resid 318 through 437 )BB318 - 437318 - 437

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