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- PDB-6wt5: Structure of a bacterial STING receptor from Capnocytophaga granulosa -

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Basic information

Entry
Database: PDB / ID: 6wt5
TitleStructure of a bacterial STING receptor from Capnocytophaga granulosa
ComponentsBacterial STING
KeywordsIMMUNE SYSTEM / CBASS / cyclic dinucleotide receptor / CD-NTase / immune effector
Function / homologyCD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain / : / NAD+ glycohydrolase / defense response to virus / nucleotide binding / CD-NTase-associated protein 12
Function and homology information
Biological speciesCapnocytophaga granulosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsMorehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
CitationJournal: Nature / Year: 2020
Title: STING cyclic dinucleotide sensing originated in bacteria.
Authors: Morehouse, B.R. / Govande, A.A. / Millman, A. / Keszei, A.F.A. / Lowey, B. / Ofir, G. / Shao, S. / Sorek, R. / Kranzusch, P.J.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial STING
B: Bacterial STING
C: Bacterial STING
D: Bacterial STING


Theoretical massNumber of molelcules
Total (without water)75,8214
Polymers75,8214
Non-polymers00
Water0
1
A: Bacterial STING
B: Bacterial STING


Theoretical massNumber of molelcules
Total (without water)37,9112
Polymers37,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-18 kcal/mol
Surface area15110 Å2
MethodPISA
2
C: Bacterial STING
D: Bacterial STING


Theoretical massNumber of molelcules
Total (without water)37,9112
Polymers37,9112
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-19 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.709, 123.709, 108.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Bacterial STING / ABC-type sugar transport system / periplasmic component


Mass: 18955.303 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Capnocytophaga granulosa (bacteria) / Strain: DSM 11449 / Gene: NCTC12948_02565 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A381HAP5
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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES-NaOH pH 7.5, 20% PEG-10000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→49.26 Å / Num. obs: 21303 / % possible obs: 100 % / Redundancy: 27 % / Biso Wilson estimate: 87.49 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 15.4
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 3034 / CC1/2: 0.619 / Rpim(I) all: 0.702

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.26 Å / SU ML: 0.5096 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.0358
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2813 1999 9.42 %
Rwork0.2325 19229 -
obs0.237 21228 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.85 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4637 0 0 0 4637
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00244708
X-RAY DIFFRACTIONf_angle_d0.48376342
X-RAY DIFFRACTIONf_chiral_restr0.0419746
X-RAY DIFFRACTIONf_plane_restr0.0028788
X-RAY DIFFRACTIONf_dihedral_angle_d17.24091776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.45421370.46371322X-RAY DIFFRACTION98.85
2.87-2.950.44061420.39111356X-RAY DIFFRACTION99.87
2.95-3.030.31421390.34071342X-RAY DIFFRACTION100
3.03-3.130.38681400.29721346X-RAY DIFFRACTION100
3.13-3.240.34941400.27461348X-RAY DIFFRACTION99.93
3.24-3.370.36181430.30711375X-RAY DIFFRACTION100
3.37-3.530.31081400.27611339X-RAY DIFFRACTION100
3.53-3.710.2791410.24021358X-RAY DIFFRACTION100
3.71-3.950.27211430.21511376X-RAY DIFFRACTION100
3.95-4.250.22781430.2051378X-RAY DIFFRACTION100
4.25-4.680.2321430.18131376X-RAY DIFFRACTION100
4.68-5.350.25661450.17911392X-RAY DIFFRACTION99.93
5.35-6.740.31241480.26131422X-RAY DIFFRACTION100
6.74-49.260.26081550.21771499X-RAY DIFFRACTION99.7
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)
16.12360243355-0.678163596153.505399656386.267690529683.343304911474.432994109950.245397865027-0.1273515416831.85498599989-0.31675613583-0.19403710498-1.36815114623-0.7807213838581.12439796721-0.05516980061980.7743693957820.03730243179790.003156918209090.645389238083-0.02551326839191.126277058195.55632412967109.3821784253.40942302331
21.131616782570.245049730409-0.3810267801690.212355244184-0.06319220854640.8724725341730.02578889721490.554477222623-0.312570767284-0.3257368148290.07669427264040.006946433884730.02264548224740.02626557899920.0002654461745380.7638834074850.1016741448240.001167795817080.813692117019-0.1128693438530.762675014465-13.004937468194.1199819431-9.17371133149
32.605583028562.328118783670.2712931001268.767292803512.587595260592.645550914610.313436447088-0.979664745667-0.5481175450031.24611770777-0.3457595545670.03393286330710.7073439394430.7997014914780.21898011130.4511360988840.0261187735640.04260353277590.7853721546160.1195367885260.637285845951-11.31122475691.4082642739.79352642647
49.794773634615.277423790142.632531194815.000154605052.633166745021.415945748510.501145426332-1.74822584987-1.266117479380.591029735962-0.8292953715380.07669763640382.0832852682-0.7374555736840.3533840264311.07789018840.09617903181110.1500151243390.6283698887320.08085477816031.14261002646-13.31390267882.50795282623.11360419169
50.4822403491060.716893320080.4481873966962.20360155155-0.4367094283351.52938150575-0.05922451750170.901248588382-0.97980609734-0.7604485860890.284411853417-0.7746747196970.8984541933860.7126261499090.07628107408881.254776422230.2613981297980.1270857716531.14970689018-0.1671848685510.90880488618-9.9582083426686.8070513713-12.1629722017
62.047820143130.201491647272-0.7152351787996.630292072272.077535537666.3954201818-0.451508192274-1.07938663199-0.748187283282-0.9819484469710.02262707179670.954495264696-0.652563173451-2.7317524503-0.1885714908661.044894477650.0126357971785-0.0497903507281.01079247761-0.03146164557410.893734342642-19.899412826688.0049356723-3.02595292853
75.83388414822.340223113181.27781079049.19526085038-2.131681913616.168633494930.276050126466-0.729952241801-0.03242315911181.32356126057-0.1704593763530.2534286011480.07184246892240.840281564697-2.053898526160.4672102030910.082132147105-0.006256770650010.713501973479-0.1100763450970.4304037904943.1419354349995.255864736111.8512695242
83.65021378464-1.67442168284-1.296010663334.91817970286-2.599657746826.06475102035-0.157777047046-0.1759256235080.9180807087420.616577517673-0.148018135237-0.199705937578-0.181896926130.384594411642-1.046018771410.7209652603020.1446821601010.03816655434270.775672824182-0.06690780014770.795130275306-7.75047286159102.5977347728.08313060374
97.79672049152-1.884159761651.339447947185.852633082211.01537131820.9092761540650.552345555575-0.7537097215520.2257802597390.1698805635950.5387424707450.8794218182690.5315386128710.2027218038454.03433367990.7209834549530.203165487117-0.200342365540.542702148613-0.1407929339230.612133562917-17.343891852398.1477230152-1.03508685894
104.323148394366.41629358785-1.839745079979.55710587506-2.810942261191.387007558521.16681542074-1.289535414720.932721570772.177968151850.203995959026-0.337877139349-0.7307305787840.3262424114561.092003955960.9842441310310.299140037206-0.08203328979550.890859808609-0.1600560983030.5979462939245.42199460535106.34531745210.8393725636
110.669534448012-0.524128989465-0.5882108889920.4012416895610.2152503032780.861095495980.145947476937-0.0556381260635-0.392643343707-0.8430535864860.0837571501449-0.1820651437720.8365483565640.2979881085950.001367737409380.9009214753770.0090417195514-0.1084237509920.7617379855310.066838897970.85146208290410.302263920386.03538192586.54792228586
123.082773125420.0442037754983-1.918658885365.107820313070.8091539973424.86533381910.4653811892460.282939593293-0.43260669933-1.341346027190.0775650958434-0.06806966431920.6480129193670.534357035090.3271585878160.5806346666550.165773343311-0.07612370151230.759656832795-0.04614153933250.64258728587615.683031638782.3933358248-2.8935752027
134.12676173139-3.52328583012-0.4346163832447.897490093971.374718009320.2561441714350.8606654168061.19130731726-0.600922338943-1.68811112347-1.48349997550.5992985639920.000931131100355-0.847407026779-0.6270642595711.136692097850.09675988905690.05539568690561.18238876374-0.2095101801040.9131261327599.3629395869581.2039522922-8.55876037329
144.329838812110.09854537664032.168910788792.651645173282.709604009743.889993210190.5182231536030.0036924632466-0.456067582206-0.433757400683-0.064846280191-0.2796237610070.8762991560340.01682998561270.1112985253360.6553380148620.05693551406050.03897194000570.6796348371440.06683342613820.9551762719376.7929552961589.2064147549-2.90624045367
155.03155523881-3.368491837751.698367846246.666784501370.0247657437652.995223820130.322667065140.2231684693011.34677786791-0.787573720887-0.402824850169-0.8073706384490.4840273987690.134191125156-0.1093081945350.598763310243-0.06266725348850.08846445387830.8447882374380.09961311520421.0126414296615.192312955399.55999844170.264995767662
162.53406655441.633277880820.5340554261976.827450701282.124521372383.423762810040.3807606924820.535355317459-0.142672882192-0.8310377180720.102365205099-0.9816388069730.455299141391.380718275551.593831586740.5782947174810.151244101231-0.1015902087890.6969241893530.05279550470481.0815991779420.55040531186.6259598190.580877127255
178.91081904376-7.28483618647-7.918118440269.394359050877.13023269848.49945504373-0.406814621481-1.19734426265-1.671730818480.8940973196020.7453409888611.700036503563.044992231930.4486748328490.509230604781.22606807955-0.305322464219-0.04592296845180.9262277526260.06154554156760.8947340563648.274803505763.84200044239.2461256809
180.111644620382-0.0462103201828-0.1835691232860.2374957438920.1457921482590.258549574857-0.341151915043-0.0290457379378-0.2493001230120.5395290075080.483913422797-0.177009266016-0.3480225354350.5624002780170.002345100435870.6394883611630.04509978119310.01564008084590.6650374738460.003954246925560.4562298566717.205544764376.551340202740.0519496184
190.902620984226-1.17769393254-0.3394552974641.549864846680.5685191235831.40346458822-0.566574244361-0.1365471562950.38020888390.5349196551730.526827289124-0.317850707675-0.5497779152270.0425842986153-0.0001449971386490.85253079729-0.0513747244856-0.05159317006740.660249211102-0.0166296112340.97050764685824.645423092290.455777898450.4011379037
203.751380008971.779988081122.658280289411.146922131951.085745152781.981951798961.137324092772.447506673460.689560161589-2.22195647739-0.0264137636293-1.223404202710.9001890522430.2846986073010.2638376053711.640178791730.2011839200880.003613064886471.456048077740.4521902571721.2277104507312.699729371186.278213205625.2478062902
210.1648537498670.2166891912560.06338053166610.2690273115920.07857271678730.0487349120286-0.1978769786711.148837711030.637538370161-2.97769989720.519086599065-1.12154054895-0.9418304978080.748463984425-0.006509209085821.768797061430.01255274718330.3717472217421.356954734630.1678487162041.3832023024920.841827394991.373333625927.2364596788
223.345036463943.26072012014-0.3077940745529.507114104991.144980869963.38315267786-0.4470681120750.174344048196-0.997946752722-0.9325862863741.09630119106-0.367825032923-0.359032905622-0.0127352017864-0.7722038689630.6682555555470.02741221521370.1464398454750.6299841289910.0818345300030.81424049584130.002659856492.304642381143.6536667549
234.871937498883.60067338026-3.215242792356.015536308611.084251123095.70156784802-0.0779974982943-0.514793420862-1.681845647880.568562915163-0.304945180921-1.101975256161.424381863560.663555480893-1.293027333840.9461214588340.1111521909440.002854350082320.887686775289-0.04654125477140.8912333028531.404107589685.760349628145.4240287953
241.844435935853.418467912111.569953548087.126621431894.337442058634.792675364930.1213901300020.1206477150720.960750075774-0.309267630572-0.2597014003310.647628469693-0.18727597465-0.755723732489-0.06553057857610.934638166179-0.148257002957-0.06505815848580.638342205162-0.05261491777221.0106435865820.982757690897.709783329643.8425423184
255.0966792520.514039153629-2.781037595883.608911065150.7469223974464.782417374670.5948066811420.2439819787880.134193444673-1.24764837076-0.483248253039-1.18109134096-0.899184291974-0.6157759878090.9254118110860.6771704175040.102774164857-0.06341353912270.6072414779120.01698930666380.527857519814.405570689375.296963351826.4284604251
260.351110471944-0.0918391965258-0.4884415104581.304885206690.6019536695210.7485844810330.0168886139833-0.219346287056-0.177778048428-0.271476681386-0.08005096499731.097456788380.476105351798-1.37060013997-0.01460856346950.788223997041-0.08501080961330.06117326861170.8799350994020.01816318763890.8013428709178.5436434683880.135683552639.4778800823
276.954513708092.37686949941-3.252203501788.19290941473.220271502624.19994204301-0.2395176885520.4167661914740.397028766357-0.0824511757068-0.3186833927481.52148181787-0.409393551136-1.19385191035-7.079658145890.559681090430.008282677297710.2055638308260.512909325483-0.07779259306320.64814291337313.195898239589.805555921744.5603887865
280.769451943662-0.222541122276-1.051132343985.76508198135-1.677519502273.878523895190.440270411389-0.0801180612624-0.5125568210290.122028372156-0.3125364113230.0608415507916-0.4917287252480.2737754212040.6347026836440.868867601035-0.034875428201-0.03897578348160.712027248754-0.0796107000510.69608289099417.003710609568.31325140230.1042953327
294.97771844971-0.5652288066541.894527751524.8703897563-0.8809661813952.7671279605-0.1467056040850.5150542700090.001634924007740.520848437916-0.278988583129-0.764680447183-1.105266363041.62366957277-0.07140661097890.832956633488-0.0622910659170.08134251480410.998889217341-0.03120638008550.76443012195134.072944486166.446065958223.864813693
304.55645126708-2.67915189745-4.087695871145.483823924561.478849092513.83891826429-0.65940600553-2.440766291691.125522666190.811969994010.602815136638-0.5830795800410.2517862196841.526865708320.3616901231921.1254301484-0.0862660357447-0.2171282514161.46257589171-0.03249692723891.3345469353839.355538136467.998388265835.8633064968
310.746813518589-0.613485547709-0.6808934790970.5813127141360.6435087683981.272791538830.9385904030220.236903148803-1.4163771039-1.475018701280.604581726581-0.951483678636-1.469579492551.384207789750.3120931939581.81165015976-0.4265846259880.2615452027971.26380576530.1848131661411.8821044766336.55030080575.865958579722.9333216868
323.553939862772.398283852751.802369648593.7174356354-0.1086186126793.06452500214-1.03757771683-0.0694582241704-1.382899523821.078224461150.470112941935-0.6375873218450.8976235188031.31324798483-3.851113659960.8105530266160.0168532516066-0.2412413556030.59914391551-0.05034269538560.86179573486526.275098170266.918446184637.1950259904
335.165165401331.35083770885-2.801412340352.954304814912.241186586884.83054811802-0.181206018799-0.159856574821-0.4680467158810.702251165547-0.266850872904-0.2166349170760.8035244590420.166531266227-0.851356549750.963734447532-0.01813179243850.02706894461430.556551642027-0.08046083158970.69023071978623.052615530659.655591405529.7280535128
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 197 )
3X-RAY DIFFRACTION3chain 'A' and (resid 198 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 228 )
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 239 )
6X-RAY DIFFRACTION6chain 'A' and (resid 240 through 254 )
7X-RAY DIFFRACTION7chain 'A' and (resid 255 through 278 )
8X-RAY DIFFRACTION8chain 'A' and (resid 279 through 300 )
9X-RAY DIFFRACTION9chain 'A' and (resid 301 through 312 )
10X-RAY DIFFRACTION10chain 'B' and (resid 152 through 158 )
11X-RAY DIFFRACTION11chain 'B' and (resid 159 through 182 )
12X-RAY DIFFRACTION12chain 'B' and (resid 183 through 209 )
13X-RAY DIFFRACTION13chain 'B' and (resid 210 through 230 )
14X-RAY DIFFRACTION14chain 'B' and (resid 231 through 277 )
15X-RAY DIFFRACTION15chain 'B' and (resid 278 through 301 )
16X-RAY DIFFRACTION16chain 'B' and (resid 302 through 312 )
17X-RAY DIFFRACTION17chain 'C' and (resid 151 through 158 )
18X-RAY DIFFRACTION18chain 'C' and (resid 159 through 170 )
19X-RAY DIFFRACTION19chain 'C' and (resid 171 through 202 )
20X-RAY DIFFRACTION20chain 'C' and (resid 203 through 209 )
21X-RAY DIFFRACTION21chain 'C' and (resid 210 through 220 )
22X-RAY DIFFRACTION22chain 'C' and (resid 221 through 230 )
23X-RAY DIFFRACTION23chain 'C' and (resid 231 through 239 )
24X-RAY DIFFRACTION24chain 'C' and (resid 240 through 254 )
25X-RAY DIFFRACTION25chain 'C' and (resid 255 through 281 )
26X-RAY DIFFRACTION26chain 'C' and (resid 282 through 301 )
27X-RAY DIFFRACTION27chain 'C' and (resid 302 through 312 )
28X-RAY DIFFRACTION28chain 'D' and (resid 154 through 170 )
29X-RAY DIFFRACTION29chain 'D' and (resid 171 through 209 )
30X-RAY DIFFRACTION30chain 'D' and (resid 210 through 228 )
31X-RAY DIFFRACTION31chain 'D' and (resid 229 through 239 )
32X-RAY DIFFRACTION32chain 'D' and (resid 240 through 278 )
33X-RAY DIFFRACTION33chain 'D' and (resid 279 through 311 )

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