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- PDB-8smg: Structure of SPO1 phage Tad2 in complex with 1''-2' gcADPR -

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Basic information

Entry
Database: PDB / ID: 8smg
TitleStructure of SPO1 phage Tad2 in complex with 1''-2' gcADPR
ComponentsGp34.65
KeywordsVIRAL PROTEIN / gcADPR / Thoeris / anti-phage
Function / homologyProtein of unknown function DUF2829 / Protein of unknown function (DUF2829) / metal ion binding / Chem-MF6 / Thoeris anti-defense 2
Function and homology information
Biological speciesOkubovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLu, A. / Yirmiya, E. / Leavitt, A. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Amitai, G. ...Lu, A. / Yirmiya, E. / Leavitt, A. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Amitai, G. / Sorek, R. / Kranzusch, P.J.
Funding supportEuropean Union, Israel, Germany, United States, 5items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Israel Science Foundation Israel
German Research Foundation (DFG) Germany
The Pew Charitable Trusts United States
The G. Harold and Leila Y. Mathers Foundation United States
CitationJournal: Nature / Year: 2024
Title: Phages overcome bacterial immunity via diverse anti-defence proteins.
Authors: Yirmiya, E. / Leavitt, A. / Lu, A. / Ragucci, A.E. / Avraham, C. / Osterman, I. / Garb, J. / Antine, S.P. / Mooney, S.E. / Hobbs, S.J. / Kranzusch, P.J. / Amitai, G. / Sorek, R.
History
DepositionApr 26, 2023Deposition site: RCSB / Processing site: RCSB
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
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

Downloads & links

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Assembly

Deposited unit
A: Gp34.65
B: Gp34.65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7923
Polymers20,2512
Non-polymers5411
Water48627
1
A: Gp34.65
B: Gp34.65
hetero molecules

A: Gp34.65
B: Gp34.65
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5856
Polymers40,5024
Non-polymers1,0832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/21
Buried area7220 Å2
ΔGint-43 kcal/mol
Surface area16080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.064, 108.064, 72.357
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Gp34.65


Mass: 10125.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Okubovirus / Gene: 34.65 / Production host: Escherichia coli (E. coli) / References: UniProt: B6V311
#2: Chemical ChemComp-MF6 / (1S,3R,4R,6R,9S,11R,14R,15S,16R,18R)-4-(6-amino-9H-purin-9-yl)-9,11,15,16,18-pentahydroxy-2,5,8,10,12,17-hexaoxa-9lambda~5~,11lambda~5~-diphosphatricyclo[12.2.1.1~3,6~]octadecane-9,11-dione / 1'-2' gcADPR


Mass: 541.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H21N5O13P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Tris-HCl, glycerol, ammonium sulfate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→39.29 Å / Num. obs: 15065 / % possible obs: 100 % / Redundancy: 27.5 % / Biso Wilson estimate: 53.7 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.022 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 26.8 % / Num. unique obs: 1204 / CC1/2: 0.743 / Rpim(I) all: 0.719 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8SME

8sme


Resolution: 2.1→39.29 Å / SU ML: 0.2866 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9576
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2499 1503 10.01 %
Rwork0.2239 13516 -
obs0.2265 15019 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.95 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 35 27 1346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021354
X-RAY DIFFRACTIONf_angle_d0.45631835
X-RAY DIFFRACTIONf_chiral_restr0.0404196
X-RAY DIFFRACTIONf_plane_restr0.0032226
X-RAY DIFFRACTIONf_dihedral_angle_d11.6849463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.37311330.34071192X-RAY DIFFRACTION98.59
2.17-2.250.33081310.30291184X-RAY DIFFRACTION99.85
2.25-2.340.40591340.30741205X-RAY DIFFRACTION100
2.34-2.440.30121340.27281203X-RAY DIFFRACTION99.93
2.44-2.570.29071340.29831212X-RAY DIFFRACTION100
2.57-2.730.33431350.27251203X-RAY DIFFRACTION99.78
2.73-2.940.35211360.28841225X-RAY DIFFRACTION99.93
2.94-3.240.2741370.25431231X-RAY DIFFRACTION100
3.24-3.710.24971380.22871242X-RAY DIFFRACTION100
3.71-4.670.19251400.1761266X-RAY DIFFRACTION100
4.67-39.290.22411510.1991353X-RAY DIFFRACTION99.87
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)
11.15078165337-0.2819382406941.212861508560.797257530315-0.4262560252710.7541274045560.281021673714-1.665370714590.6460009752340.373419492903-0.178660720906-0.122116858584-0.4723184407660.01808400865560.001487973998760.552592825893-0.0753014564950.005066403510750.919839043747-0.0181648431790.505717043086-30.102626334323.6891407266-4.18635160105
20.5382532547570.01977763407090.38939811706-0.0589192585470.06024542394850.164164944380.445382482442-1.473495831550.805618497046-0.122383785436-0.419688878482-0.5252157353340.12065796992-0.2258530642850.0007239937343880.666413995714-0.0210697141019-0.008163176555160.811064325350.0001757938398920.726976503497-53.879431413921.8899534186-10.9706932141
30.114610107575-0.03567250450410.1344565449630.1674312144520.1067746098090.2439658122430.0475635305610.230273482498-1.97346475862-0.0374727484474-0.1000653667670.6260701438191.15477668662-0.41882162404-0.0003349724925370.6742626435530.0226993243929-0.005571779718170.8780526076530.04522180692150.963905618199-49.410116016814.7136756039-14.0452645719
40.128767115744-0.2031763261410.3313525881280.404517002936-0.5696064443040.66303830560.0160113341513-0.357417853271.671538025010.542332578625-0.3562887420050.125187880901-0.6390492825650.5209215700750.0005652336062730.52224728820.015161227079-0.02293848522590.6249043153210.09771918252260.701977464987-32.864985055729.3707517884-14.1233520256
50.1346393051840.05789387939290.05403547168030.080885075411-0.005220362609220.002261666614720.2082014936640.2155678312820.323913625289-0.680543574086-0.650292333902-0.4921391314920.1794415115460.300337806283-0.001330859533110.5062489442630.1195655721540.04359106746950.6369197872190.04324763352950.659306654674-30.527847186922.6423361257-15.0902843442
60.448358743416-0.2914638610630.1746099161291.278035168750.1786892532560.1656736861330.152576166755-0.6104561041380.7655013226460.1696390405840.229358817634-1.63154192838-0.09563224291010.3241436587160.0262408421530.590729196626-0.0425893778012-0.08344823010730.8567329188730.03704530548330.638442485849-24.032370158220.8241304023-4.0517354019
71.26053292608-1.06989548661-0.6765158571212.906843234780.1821617215126.54746848333-0.224212162099-0.700761559536-1.17532929943-0.0623586769269-0.512521050757-0.11384442040.2445034504660.097032928219-2.502138893810.5298223840520.01454732869150.05523729833290.6344787436910.3236178518260.757229523157-27.09240064032.45761122306-8.94317937881
80.05959848907250.00283805854449-0.375348507180.01466773698750.2391279329082.435932816090.965894273947-0.569402620527-1.238150502330.4286029807570.0747462669598-1.13089403517-0.6164055570670.1670518911840.06152146384490.79238679623-0.188637131924-0.1496965221431.4608707540.4737077473011.52189865866-6.9971996393611.7721095785-11.8281914086
91.984221394620.9944809756270.960515242962.08204544233-1.73748543631.907823505910.127369146474-0.396310471629-0.80721511083-0.0132925485375-0.359409663075-0.1908258188160.1886335488850.173410946173-0.04154550458220.4472454564080.0404477937830.07032638416130.5242804757240.1619142729650.668956376574-27.50455078854.82942160174-14.3171149805
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 36 )AA4 - 361 - 33
22chain 'A' and (resid 37 through 51 )AA37 - 5134 - 48
33chain 'A' and (resid 52 through 59 )AA52 - 5949 - 56
44chain 'A' and (resid 60 through 69 )AA60 - 6957 - 66
55chain 'A' and (resid 70 through 76 )AA70 - 7667 - 73
66chain 'A' and (resid 77 through 89 )AA77 - 8974 - 86
77chain 'B' and (resid 4 through 35 )BB4 - 351 - 32
88chain 'B' and (resid 36 through 59 )BB36 - 5933 - 46
99chain 'B' and (resid 60 through 89 )BB60 - 8947 - 76

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