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- PDB-8bao: Dysgonamonadaceae bacterium CRISPR ancillary nuclease 2 -

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Basic information

Entry
Database: PDB / ID: 8bao
TitleDysgonamonadaceae bacterium CRISPR ancillary nuclease 2
Components
  • Cyclic tetra-adenylate (cA4)
  • DUF1887 family protein
KeywordsDNA BINDING PROTEIN / nuclease / homodimer / can2 / CRISPR ancillary nuclease / cyclic tetra-adenylate
Function / homologytRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / nucleic acid binding / BROMIDE ION / RNA / DUF1887 domain-containing protein
Function and homology information
Biological speciesDysgonamonadaceae bacterium (bacteria)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLi, A.W.H. / Doherty, A.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S008691/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M008800/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P007031/1 United Kingdom
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Reverse transcriptases prime DNA synthesis.
Authors: Zabrady, M. / Zabrady, K. / Li, A.W.H. / Doherty, A.J.
History
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF1887 family protein
B: DUF1887 family protein
C: Cyclic tetra-adenylate (cA4)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0017
Polymers90,6573
Non-polymers3444
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-20 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.133, 109.429, 63.043
Angle α, β, γ (deg.)90.000, 101.880, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-657-

HOH

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Components

#1: Protein DUF1887 family protein


Mass: 44692.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dysgonamonadaceae bacterium (bacteria) / Gene: C0T31_04800 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2N4S908
#2: RNA chain Cyclic tetra-adenylate (cA4)


Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#3: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.89 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole; MES monohydrate (acid) 0.03M Sodium fluoride; 0.03M Sodium bromide; 0.03M Sodium iodide 20% v/v Glycerol; 10% w/v PEG 4000 208.3uM cA4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.058→54.715 Å / Num. obs: 63804 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.08 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.1 / Rrim(I) all: 0.26 / Net I/σ(I): 5.1
Reflection shellResolution: 2.058→2.093 Å / Rmerge(I) obs: 2.405 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3196 / CC1/2: 0.342 / Rpim(I) all: 0.963 / Rrim(I) all: 2.593 / % possible all: 100

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
pointlessdata scaling
PHENIX1.20.1_4487refinement
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.06→54.71 Å / SU ML: 0.3194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1276
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 3126 4.91 %
Rwork0.2198 60482 -
obs0.2216 63608 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.1 Å2
Refinement stepCycle: LAST / Resolution: 2.06→54.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 88 14 327 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086228
X-RAY DIFFRACTIONf_angle_d0.95388427
X-RAY DIFFRACTIONf_chiral_restr0.058923
X-RAY DIFFRACTIONf_plane_restr0.00711080
X-RAY DIFFRACTIONf_dihedral_angle_d8.0167848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.090.33681390.30692642X-RAY DIFFRACTION96.76
2.09-2.120.35341370.30332712X-RAY DIFFRACTION98.45
2.12-2.160.34911410.29382744X-RAY DIFFRACTION99.48
2.16-2.20.32211230.27522726X-RAY DIFFRACTION99.69
2.2-2.240.3471240.28082766X-RAY DIFFRACTION99.79
2.24-2.290.34811390.26872754X-RAY DIFFRACTION100
2.29-2.340.32011490.26052760X-RAY DIFFRACTION99.86
2.34-2.390.28451380.25592731X-RAY DIFFRACTION100
2.39-2.450.27921570.2482736X-RAY DIFFRACTION99.97
2.45-2.520.32711530.24432739X-RAY DIFFRACTION99.76
2.52-2.590.30691310.23682762X-RAY DIFFRACTION100
2.59-2.680.33641300.24122763X-RAY DIFFRACTION99.97
2.68-2.770.27131410.22832748X-RAY DIFFRACTION100
2.77-2.880.28431530.21842782X-RAY DIFFRACTION99.93
2.88-3.010.22941490.21542732X-RAY DIFFRACTION99.93
3.01-3.170.27721410.21632761X-RAY DIFFRACTION99.79
3.17-3.370.23541520.20722727X-RAY DIFFRACTION99.86
3.37-3.630.26271400.19722764X-RAY DIFFRACTION99.83
3.63-40.19871460.19892751X-RAY DIFFRACTION99.97
4-4.580.21221400.18512780X-RAY DIFFRACTION99.97
4.58-5.760.23091400.20392807X-RAY DIFFRACTION99.97
5.77-54.710.21731630.2142795X-RAY DIFFRACTION99.8
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)
10.804521707804-0.388164672177-0.3546510656440.9457268964880.2005306864070.1576756307220.05765171380460.01308339919890.09256847598150.0309787316731-0.0165308994083-0.0391876070109-0.01758042293080.002834828864811.37796038712E-50.314594970422-0.0134566381878-0.008521391252660.276078577273-0.005373647975440.264078102216-53.483359690712.265634874218.6109050069
20.000359858746542-0.005761064740950.002738020584590.0288004462096-0.01745288829430.00991034389515-0.0935682688174-0.159108695982-0.2737335228170.2966189552260.104807610346-0.1351471361730.0144561773859-0.1526098512010.0003312737203050.3152556686690.01614769298280.03983395785840.3457809704870.003614501866130.289017402584-34.6771852045-13.640747928810.1720954588
30.2054919298110.2292464482140.1708874444820.466391882968-0.07843268052340.5791505071340.0151378206299-0.0437842678396-0.112963388930.0582104829274-0.0228802240959-0.001167036986150.07076741121170.009645801726549.88655253998E-60.3201920018310.02092141047470.008630638529880.3068402748710.0127454875950.317616295969-36.526097286-28.361609505116.9116095852
40.947461798892-0.5887579958790.4228473958690.516362298179-0.3849165447830.3436856254980.01732188940660.0786386977129-0.0326120682535-0.0896345890512-0.002897822912430.07241761935160.08106726300150.0206438548632-2.13478261105E-50.3309020620840.00044076237998-0.03167158319710.325358732634-0.004099564080310.291695913268-56.5573142686-7.40950303229-9.10324281996
50.6635552084050.348057324019-0.3955239223261.040415301790.1119449582360.632621990033-0.0370562333920.004771122777310.07359192668860.002491833128560.0138622881293-0.27379607488-0.07017505575480.1719594683613.98880967238E-50.254488898571-0.00370707432691-0.005124629767190.372559136630.02621725930130.386158797256-20.6755257391-9.020949644610.2051801232
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 140 through 367 )BC140 - 367140 - 367
22chain 'C' and (resid 1 through 4 )CE1 - 4
33chain 'A' and (resid 0 through 110 )AA0 - 1101 - 111
44chain 'A' and (resid 111 through 367 )AA111 - 367112 - 368
55chain 'B' and (resid 1 through 139 )BC1 - 1391 - 139

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