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- PDB-9ciw: Penguinpox cGAMP PDE H72A mutant in complex with 2'3'-cGAMP -

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Basic information

Entry
Database: PDB / ID: 9ciw
TitlePenguinpox cGAMP PDE H72A mutant in complex with 2'3'-cGAMP
ComponentsPenguinpox cGAMP PDE
KeywordsVIRAL PROTEIN / immune evasion / phosphodiesterase
Function / homologyCyclic phosphodiesterase / : / Uncharacterized protein
Function and homology information
Biological speciesPenguinpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHobbs, S.J. / Nomburg, J. / Doudna, J.A. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: Cell / Year: 2024
Title: Animal and bacterial viruses share conserved mechanisms of immune evasion.
Authors: Hobbs, S.J. / Nomburg, J. / Doudna, J.A. / Kranzusch, P.J.
History
DepositionJul 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation
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_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penguinpox cGAMP PDE
B: Penguinpox cGAMP PDE
C: Penguinpox cGAMP PDE
D: Penguinpox cGAMP PDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6906
Polymers91,4654
Non-polymers1,2252
Water8,467470
1
A: Penguinpox cGAMP PDE
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 23.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)23,4792
Polymers22,8661
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penguinpox cGAMP PDE


  • defined by author
  • 22.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,8661
Polymers22,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Penguinpox cGAMP PDE


  • defined by author
  • 22.9 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)22,8661
Polymers22,8661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Penguinpox cGAMP PDE
hetero molecules


  • defined by author
  • 23.5 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)23,4792
Polymers22,8661
Non-polymers6121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.967, 64.963, 196.424
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Penguinpox cGAMP PDE


Mass: 22866.209 Da / Num. of mol.: 4 / Mutation: H72A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penguinpox virus / Gene: pepv_029 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A068EGP0
#2: Chemical ChemComp-A1AWU / [(2~{R},3~{R},4~{R},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl [(2~{R},3~{R},4~{S},5~{R})-2-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate


Mass: 612.447 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H25N10O11P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 200 mM magnesium formate 24% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jun 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→63.39 Å / Num. obs: 34185 / % possible obs: 99.6 % / Redundancy: 13.5 % / Biso Wilson estimate: 31.41 Å2 / Rpim(I) all: 0.016 / Net I/σ(I): 17.2
Reflection shellResolution: 2.4→2.45 Å / Num. unique obs: 2580 / Rpim(I) all: 0.282

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→63.38 Å / SU ML: 0.2972 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5653
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2489 1657 4.86 %
Rwork0.1952 32472 -
obs0.1978 34129 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.33 Å2
Refinement stepCycle: LAST / Resolution: 2.4→63.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6390 0 84 470 6944
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00146604
X-RAY DIFFRACTIONf_angle_d0.40458966
X-RAY DIFFRACTIONf_chiral_restr0.04091024
X-RAY DIFFRACTIONf_plane_restr0.00281140
X-RAY DIFFRACTIONf_dihedral_angle_d12.71892464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.470.3021310.23442580X-RAY DIFFRACTION97.24
2.47-2.550.30381280.23652645X-RAY DIFFRACTION99.39
2.55-2.640.29041230.23632679X-RAY DIFFRACTION99.75
2.64-2.750.33261420.23112686X-RAY DIFFRACTION99.72
2.75-2.880.25841480.24042658X-RAY DIFFRACTION99.75
2.88-3.030.34881230.23492693X-RAY DIFFRACTION99.44
3.03-3.220.30761360.21862709X-RAY DIFFRACTION99.93
3.22-3.460.26111370.20392707X-RAY DIFFRACTION99.93
3.47-3.810.22531370.18382707X-RAY DIFFRACTION99.93
3.81-4.360.24551340.16042749X-RAY DIFFRACTION100
4.37-5.50.18591730.15842745X-RAY DIFFRACTION100
5.5-63.380.20151450.1722914X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
17.82189701564-8.17502138105-0.5109358779829.385008914060.009991219960362.14591563095-0.44506471434-0.7092281497330.08077990507230.8604133645570.6333671792580.113388656483-0.115169515930.207747916842-0.1219234737080.314278023686-0.04973074102420.02697601200290.330649099171-0.07048439362640.21501599467749.089230922325.1915391634-27.1065830579
21.37677738359-1.2467745739-0.6970135104821.67177515249-0.8898828287923.424530039970.2699798746840.4339595659060.2652383711310.08578989210530.2730385492290.25603474529-0.633013241889-0.779950751916-0.5131623035350.2692553855930.05147416324830.05754973535910.387397810871-0.01624336085440.24187346738521.072425040926.0823895593-26.1480629442
36.360186040623.7179049697-1.723005870693.58369628059-1.328423536871.223962197171.14161583025-0.942133036371.275898773960.905442529787-0.4492736387650.382225008945-1.223843323630.173502117145-0.3354954446860.5851365469-0.06591814884370.2301096022190.347256239624-0.09491294610630.50727495026928.030079519633.7903404779-13.2286017836
40.6576650341480.0200742426308-0.007110586087610.0897983820614-0.6094382165023.496545621370.3836414214430.04043418936430.297048874947-0.126756295925-0.08818898811040.0030885323065-0.6633127836190.0717559789321-0.2593627074540.3910821219410.02184611274620.1112662838720.251516818361-0.00529853255790.31616437840828.809358801930.7327374605-26.328165844
52.815688749930.896005610581-1.438226252952.14032220387-0.2817354878055.194033110450.111383003370.336198991055-0.117889152269-0.26801040380.03131574157180.03068700393420.0199950246917-0.529062124409-0.1097099700970.1770111439750.0985507535173-0.01168438614070.185000915887-0.01077784901240.24645636333227.247222434420.7935913099-33.21475835
63.352341332251.819033104220.4562668760940.9363005610280.2557014554670.01790408928170.322078901964-0.5867307747980.0593916012903-0.118296105464-0.0683455022175-0.2492289556630.1489179597890.0529159088743-0.1585030915560.2820688314380.05572116094950.02092517492720.292044949125-0.02584616155980.32885559706738.06471881118.0754559479-32.3548193475
75.19116756184-0.2524225424-0.2070852258541.35774413142-0.701589460916.852172748990.0351028165957-0.37980168925-0.2027392245680.4119827812470.1208987079930.00163636137681-0.01973606526090.126835676746-0.1947929030770.2839997431250.009137418842110.05304113373390.2227362108880.007132322997320.2779555445725.306577528620.3991969166-12.4047425875
82.238887645231.27301839217-1.064607650168.13040048745-4.763797805353.67782015515-0.02117385818960.302142445439-0.1130474230030.6059802101860.1327691204130.205632781929-0.0373374092661-0.849631762265-0.1282513891310.3095048009960.0287855558733-0.014885210510.3792704690890.00919127983520.40497216992116.740175324819.2104120669-30.8733443949
96.041702839581.484448859391.918274674410.969165658204-1.240251234575.913219593830.5693103641511.28182849344-0.554552288261-1.10369673834-0.239601251273-0.7845819457060.5818274070620.801893316783-0.07925213307330.6755444755170.01552183135830.2549054586760.457914214604-0.1226845589370.34909522374936.0520508-25.3325769695-2.81989907933
102.04308813108-0.2731591001370.6924321480571.23143303888-1.804176953863.401552066470.02656287724140.1845307900240.054037324731-0.08291922311-0.0858079833482-0.03921582345320.1148890516570.1861404728370.07006524871060.304654630310.0390796661141-0.051863260130.3147323958680.01712127654790.2439181185135.04587259287.69025575462-10.1173312284
116.07023856523-0.133452998053-0.05194958386273.467973654094.958035134427.954831756920.4271035467370.800290808328-0.302075157080.401080811613-0.8238982064480.7691890492720.67496825989-0.3161796556140.4555562620510.5526462017570.0318732589625-0.1100843689730.4101043408730.01874283914160.41448496262132.1531985225.37042228008-14.328765721
121.428250798221.1538954888-1.687331520826.499073980060.02919923770152.21277013717-0.2668192997590.3954024658560.161912807378-0.394118164288-0.06450575858281.22392326903-0.181030762281-0.5004160193550.1602383807320.3018205367760.0285510701682-0.1020897389130.3622624499430.02455531233840.37118057180122.5064434116-1.969047644795.22913119093
131.620525450310.5186959500181.28254622831.56218514375-1.097388184862.935520124140.1080618328730.110834061326-0.155530477581-0.0946606486409-0.1938216185590.008199570720620.01343216042020.3196909445810.0882997164370.2688467853820.0361254372773-0.04126170614690.181967040334-0.0169731419330.2542632363737.42376484072.65996012141.24695967164
14-0.02111553804750.616087305842-0.08699931484043.37023049488-0.35792024560.00474151785198-0.04122248902150.07077560296640.217780060266-0.412133314684-0.12854432018-0.5425814855230.2770574915090.1646198776720.09738504314340.3958684224460.01478829347480.07070580883030.2753506727640.05653171477760.37366029975937.1655856387-11.06564639124.08021569971
152.76316528545-0.3825512097950.523199058782.424721553240.3066651505590.4220652174250.2716202498121.268873866890.110108543597-0.138556540102-0.434321133364-0.5424945763470.02755454426311.329842724250.2179314462770.253004671664-0.0104341049427-0.01834800227110.764316431470.1920555881590.3625154018547.550199555810.2522844801-10.7851943613
163.748714894-1.69113843937-2.478120337163.956904561960.05679521504413.4123518939-0.129926052318-0.07783624846290.98529602830.0924105621670.1621963789130.161163178271-0.412403645638-0.009617163236630.04703105091560.3561487299150.0459261842618-0.09294285375030.1958798235310.08298790403270.37876830450734.357844305311.06479108614.95009141711
174.25639824045-1.756107143060.1084234892938.820171136921.152288526073.398599162550.0835615199039-0.707707870335-0.4377834437951.260565238320.09705756398760.3523045755810.3242768673950.76484067127-0.09662720127940.585357354245-0.0389439852727-0.09184427081220.5866256196840.1152788430490.3371252391742.0939499021-18.5568491284-46.8918315121
182.136343259850.511169028544-1.229969265541.88612602844-0.5943095426263.5741867646-0.0106219295402-0.02205959353740.1503819926720.4028739579840.2378570167450.00706459524811-0.507406798549-0.117227215518-0.2408580154980.3498697697420.1093801731140.02090094637080.266739146542-0.0148253571720.2445936329279.44253183089-16.4974233295-39.0391458034
194.15155828806-1.106425985323.929370353634.17817140564-0.1800316311114.46164302155-0.5031928167820.2345644842440.9665476518630.4457018112840.459273815079-0.314972571896-1.087897560940.9096707063320.02314117424180.3730674338190.003051239308320.0305103250210.559195859573-0.03181689023070.45139494167811.9581640978-13.7459052466-34.8806883563
203.795423618931.32348671005-1.280691902482.22091686522-0.6107931896353.095116958650.1050642151690.2310536124210.6544943308990.1041388505010.161843215380.160226431722-0.636339934714-0.191490153017-0.1585763956010.2492033471370.06832485476880.03909349329090.2464713775260.0234426603480.28295706727814.3320963563-9.84296419976-55.6106647359
211.82147950105-0.1547926325890.3916515650633.45526107462-0.8523359183762.83658738156-0.193806547619-0.3612228803420.1618200779180.4049405172530.154283320249-0.737398242609-0.009393665312170.811121865561-0.006730304158710.2859991977290.122433616539-0.07530517973230.461560148047-0.07688761029020.34411948306516.108109275-23.5778849337-38.6810973876
222.632867932-0.0269066213383-0.5877410680720.07494028353170.1983628887920.3861073578790.0293543863596-0.218765067665-0.314211493855-0.1711679387210.017108194438-0.09337746767360.1096059547740.05325824050730.007240272631380.264136829637-0.01295344945970.04080126308790.2294392737120.04432240814320.28516280099423.8121507238-16.5488394425-57.1539866785
232.29766653221-0.45622340597-0.3294809186093.2472764305-1.680389642114.82303141583-0.265808593606-0.681295879487-0.5083810502610.4576144917190.321591786553-0.1370951519230.5218868486770.482077150008-0.06095918784520.3102968467930.1070478250780.04685189417880.3431828571290.03610223425590.2322788850786.51204657638-28.8901939637-38.7307697004
242.222482439080.113490126678-0.5525433883284.870617808790.347469214762.528401621070.08788139524470.4133900545460.1330822601720.9553123400970.4632189912020.955179244897-0.0797321394515-0.6207170119550.2092190583630.30086377650.07032461470280.04015569928670.195253104246-0.05466693537710.2742118698755.97062187856-15.5978573149-54.023327227
258.35551060973-5.56726550439-1.070124839666.85879440007-0.4926473612811.046466780630.09876955922880.8860805011890.105857488005-0.678939526107-0.1916808858710.1884831582280.04155721348250.004802705154480.09042585912620.329330629596-0.0589415873886-0.02214746523890.310662677797-0.04550726122310.207760014546-6.99873320172-31.4938408463-21.949694324
261.83734446977-0.384081359716-0.09558253550332.91179584775-0.7910573170674.03624500815-0.01572870079280.1457399644870.104168970776-0.05793724864250.1008898193570.349616106431-0.0399181099938-0.461420273421-0.09357263877630.1919049800320.04733058369970.007213484871140.2918077049510.04131995697410.263509459458-13.5110851343-7.8441062955-26.9702389275
271.444857216680.3434814485510.2355741102914.142742044890.2972091489652.562928377160.138279749258-0.1772678762110.2481472942670.6166121154640.06262178823380.203283504456-0.3722598605510.00894459579223-0.1198828261370.2897767517670.0556657787069-0.02965198115840.259983625352-0.04784882401770.238042415037-5.67866584002-6.26240092913-10.3178610116
281.055835073810.3421522171010.02522821827531.87629111679-0.9886523702463.44005920279-0.01608905158060.06915503330730.0002429869639420.0764158536508-0.0882003694938-0.2111179369570.2667551613710.02884763012980.1093459270340.2432079795910.03398701387480.03933846226820.151389583274-0.01183464641610.246410735697-2.94027976749-13.4076056218-20.6130767229
290.02940523545850.864505360908-0.03098850639614.61074298212-0.193170391475-0.0342830071713-0.07509920990910.129053314639-0.108368333501-0.508114405147-0.188382340499-0.723362701512-0.1141208779290.08569126507230.204989008350.3630275605190.0776787689683-0.04254764803570.3585640029910.01513727613860.320350058635-0.655922613769-20.19755025-16.3268769226
302.81752851643-0.639369027703-0.09417622336275.68471149488-0.7574245188055.095966281960.1648265157480.5941064806050.028618961315-0.359625940272-0.008075688188380.1913576903570.02336609260240.256453121912-0.2203166273190.1595755554990.05918732266510.03742798147180.3068224157640.02953245917950.210313664533-3.50143750923-7.15897453898-36.0052585715
314.72867029340.456801405453-3.699338573243.70459369079-1.211851796783.615874023370.299395047020.2372406853460.5322436596210.5707580932880.02285548267910.0198144594681-1.27578671846-0.372245623757-0.4254989157860.4141885209480.0572341541975-0.05575744019280.337150525551-0.0104334784080.40052639111-2.818090104621.16645766921-17.4113226328
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 19 )AA1 - 191 - 19
22chain 'A' and (resid 20 through 39 )AA20 - 3920 - 39
33chain 'A' and (resid 40 through 54 )AA40 - 5440 - 54
44chain 'A' and (resid 55 through 79 )AA55 - 7955 - 79
55chain 'A' and (resid 80 through 147 )AA80 - 14780 - 147
66chain 'A' and (resid 148 through 166 )AA148 - 166148 - 166
77chain 'A' and (resid 167 through 191 )AA167 - 191167 - 191
88chain 'A' and (resid 192 through 203 )AA192 - 203192 - 203
99chain 'B' and (resid 3 through 17 )BC3 - 171 - 15
1010chain 'B' and (resid 18 through 54 )BC18 - 5416 - 52
1111chain 'B' and (resid 55 through 71 )BC55 - 7153 - 69
1212chain 'B' and (resid 72 through 92 )BC72 - 9270 - 90
1313chain 'B' and (resid 93 through 147 )BC93 - 14791 - 145
1414chain 'B' and (resid 148 through 166 )BC148 - 166146 - 164
1515chain 'B' and (resid 167 through 191 )BC167 - 191165 - 189
1616chain 'B' and (resid 192 through 203 )BC192 - 203190 - 201
1717chain 'C' and (resid 3 through 17 )CD3 - 171 - 15
1818chain 'C' and (resid 18 through 54 )CD18 - 5416 - 52
1919chain 'C' and (resid 55 through 71 )CD55 - 7153 - 69
2020chain 'C' and (resid 72 through 110 )CD72 - 11070 - 108
2121chain 'C' and (resid 111 through 134 )CD111 - 134109 - 132
2222chain 'C' and (resid 135 through 166 )CD135 - 166133 - 164
2323chain 'C' and (resid 167 through 191 )CD167 - 191165 - 189
2424chain 'C' and (resid 192 through 203 )CD192 - 203190 - 201
2525chain 'D' and (resid 1 through 19 )DE1 - 191 - 19
2626chain 'D' and (resid 20 through 71 )DE20 - 7120 - 71
2727chain 'D' and (resid 72 through 110 )DE72 - 11072 - 110
2828chain 'D' and (resid 111 through 147 )DE111 - 147111 - 147
2929chain 'D' and (resid 148 through 166 )DE148 - 166148 - 166
3030chain 'D' and (resid 167 through 191 )DE167 - 191167 - 191
3131chain 'D' and (resid 192 through 203 )DE192 - 203192 - 203

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