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- PDB-6xb5: Structure of Trichoplusia ni poxin in post-reactive state with Gp... -

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Basic information

Entry
Database: PDB / ID: 6xb5
TitleStructure of Trichoplusia ni poxin in post-reactive state with Gp[2'-5']Ap[3']
ComponentsPoxin
KeywordsHYDROLASE / Poxin / nuclease / HDD13 / Lepidoptera / Moth / Butterfly / innate immunity / cGAS / cGAMP / STING
Function / homologyPoxin, virus / 2',3'-cyclic GMP-AMP binding / nuclease activity / 2',5'-GpAp / Uncharacterized protein LOC113495595 isoform X1
Function and homology information
Biological speciesTrichoplusia ni (cabbage looper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.
CitationJournal: Elife / Year: 2020
Title: Structures of diverse poxin cGAMP nucleases reveal a widespread role for cGAS-STING evasion in host-pathogen conflict.
Authors: Eaglesham, J.B. / McCarty, K.L. / Kranzusch, P.J.
History
DepositionJun 5, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poxin
B: Poxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2034
Polymers53,8182
Non-polymers1,3852
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-1 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.422, 124.422, 132.178
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METLEUA1 - 240
d_21ens_1METLEUB1 - 240

NCS oper: (Code: givenMatrix: (0.646743277496, -0.75061380722, -0.135285052478), (-0.748798033627, -0.658601089383, 0.0744722089084), (-0.1449987512, 0.053136780803, -0.98800396997)Vector: -18. ...NCS oper: (Code: given
Matrix: (0.646743277496, -0.75061380722, -0.135285052478), (-0.748798033627, -0.658601089383, 0.0744722089084), (-0.1449987512, 0.053136780803, -0.98800396997)
Vector: -18.4429001144, -29.5529194922, -59.2866331728)

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Components

#1: Protein Poxin


Mass: 26909.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichoplusia ni (cabbage looper) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A7E5VPD6*PLUS
#2: Chemical ChemComp-9BG / 2',5'-GpAp / [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl [(2~{R},3~{R},4~{R},5~{R})-2-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl] hydrogen phosphate


Mass: 692.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H26N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
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: 4.85 Å3/Da / Density % sol: 74.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM HEPES-KOH, 32% Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99995 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99995 Å / Relative weight: 1
ReflectionResolution: 2.89→39.57 Å / Num. obs: 22422 / % possible obs: 99.6 % / Redundancy: 15.2 % / Biso Wilson estimate: 76.18 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.068 / Net I/σ(I): 9.5
Reflection shellResolution: 2.89→3.07 Å / Redundancy: 14.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3527 / CC1/2: 0.372 / Rpim(I) all: 0.854 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phased with Companion Structure 6XB6

6xb6


Resolution: 2.9→39.57 Å / SU ML: 0.4402 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.3569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 2006 9.06 %
Rwork0.1841 20129 -
obs0.1869 22135 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 75.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3726 0 92 0 3818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00623922
X-RAY DIFFRACTIONf_angle_d0.93455358
X-RAY DIFFRACTIONf_chiral_restr0.053586
X-RAY DIFFRACTIONf_plane_restr0.0064692
X-RAY DIFFRACTIONf_dihedral_angle_d21.50161382
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.736522808254 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.371360.35711335X-RAY DIFFRACTION91.48
2.97-3.050.36361390.32751427X-RAY DIFFRACTION99.68
3.05-3.140.33281480.3081451X-RAY DIFFRACTION99.94
3.14-3.250.34181290.2871451X-RAY DIFFRACTION100
3.25-3.360.31791450.25911415X-RAY DIFFRACTION99.94
3.36-3.50.25771450.23311436X-RAY DIFFRACTION99.94
3.5-3.650.23591460.21371452X-RAY DIFFRACTION100
3.65-3.850.23381510.20661425X-RAY DIFFRACTION100
3.85-4.090.20521480.15651459X-RAY DIFFRACTION100
4.09-4.40.17511460.14921456X-RAY DIFFRACTION100
4.4-4.840.14931500.12771416X-RAY DIFFRACTION100
4.85-5.540.16981410.14191465X-RAY DIFFRACTION100
5.55-6.980.19611420.16991466X-RAY DIFFRACTION100
6.98-39.570.17771400.14741475X-RAY DIFFRACTION99.26
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)
11.17246152576-0.411531919862-0.253606685911.5593850017-0.7012030318241.49960884470.00546967920023-0.1874507743630.105432307655-0.1144122955620.137067941458-0.346728868762-0.499700780901-0.1405430954860.005544560101480.4805363469690.08737447262950.08748452957690.3459139626450.06779465415530.32823664455517.2089922781-11.9248060583-35.0221400388
20.363459419749-0.1847646004780.1911968677740.08833429205530.2379710794070.590711894170.3760894323020.723029315437-1.40021678629-1.18486447756-0.598594773678-0.3612183653980.487120955663-0.568806274064-0.0001802370973260.8688363288550.09245491280870.00436801054780.66471592296-0.2585438000691.0395013774220.0073287863-37.2369255707-49.490163259
32.21624048022-0.625666615223-1.136087547850.4775253592240.3828634146320.8557551861150.2710957834110.5660298514430.361653691195-1.78006656399-0.499747373928-1.775170716880.6222699333770.2830084855680.02784745589630.4909148405430.1207707310290.2198423406760.4679138960180.07700790449710.96888522583226.4934813363-29.0314307984-40.644475952
4-0.2133694474140.4428780111690.1445580112140.911518565831.066425385862.283208235460.02603886949070.1223642982090.0213928728703-0.9762754530620.108400504323-0.4096746276830.260227208639-0.582324018375-0.1676418659730.5712379705830.06511291380050.2361337203680.3939386838720.09516445135090.55605488293518.9174156081-24.162424462-40.2391428157
51.21795232999-0.2421605743590.4502242335770.992842295411.504270501842.65328803079-0.56044771781.29591053723-0.008986940130660.6987468978410.8087878956481.287253841620.79274111589-1.495669987431.362822244420.617214046341-0.2768272369050.1470997429891.091280122880.381213699390.951383016231-12.1510828303-48.5433556578-20.9722959555
60.362213424582-0.150983531722-0.428162774170.6525150693180.6408495765510.498291241764-0.02410760986830.103640240326-0.402868841958-0.07078757920050.1073377985570.198847463790.828763602288-0.6762503259280.000513197911090.909341186942-0.306246132666-0.04250615847741.115590127760.1675973542830.972213185547-4.06553365481-52.4650026779-27.531359126
71.61807969613-0.7433046175320.05916737950820.49883302391-0.1279005327270.2886449724620.1150539743380.472756008-0.581779598568-0.7255947960580.148105234951-0.1825542201970.5105600250480.3484305848140.003838648208750.844580818697-0.110569843640.07800996682910.7108164267930.05199412071220.7428594624229.67111016199-48.7216199782-33.886865364
80.7086457515970.2175481694630.228399776730.3707168824330.8344238983630.684951699917-0.08365900636080.464615639337-0.186346407294-1.46883517150.5509601539790.4857186483060.442518251312-0.496967785702-0.003295394720580.816260003932-0.204429918956-0.1750290230411.058417312740.2143056333940.755482209631-8.49028648974-41.8850102228-33.8363988892
90.1777378552890.366667235323-0.4703628407970.962474773292-0.4014583998140.959691439869-0.1762269999380.3797763609480.22583443452-0.1971094628990.368144470438-0.09029966804920.166476729563-0.5647797910690.02947395663070.568990357594-0.0850703420430.02594898106310.6969526294370.1976840028250.5414270724460.821815893382-37.6506002806-29.4857405944
100.803376233278-1.30843594167-0.9403405099611.666399507720.03630931777891.496973199070.451052437759-0.0926819789026-0.147954569407-0.599824851686-0.1202265266460.0286353091628-0.321768907068-0.2782335578030.5244861253460.595997751953-0.0424107117228-0.01404158934190.8055522087990.1411780702820.6095417622320.533844520615-37.0153133265-28.6879693045
111.457498011270.3611035389660.2554154015141.59951873014-0.5408571650220.2556434104720.0115449946403-0.415900495207-0.466921682641-0.063456140251-0.250181692244-0.2222735848060.282924691061-0.300811523476-0.005426176952880.460219128480.0137593361418-0.0005397218357830.4500224468680.1310835440810.51366051324121.3479544575-31.4896635825-20.6374538126
120.124926616970.215489505439-0.4555312500220.439849012871-0.6515969684790.894292179264-0.0335739490259-0.57550952145-0.7193681000971.35376248040.251049517568-1.198082239271.030863549171.003310905580.01763958433950.6894320617960.0358306445698-0.1005304415430.7750083463860.1236771632050.89362906117332.9876178927-27.6089842752-22.1479541044
130.531271429881.350434235930.4001045844951.51366365506-0.4356009250531.761765137820.0849941247259-0.0537911829577-0.4815340279910.577664326809-0.147833187767-0.3412831472770.00325330869442-0.0596858956265-0.3717288257550.4314651838020.06220064150220.02738830401950.5660673131170.1894116587770.5399451691717.2214448884-30.7429524699-22.6672479269
140.33658744325-0.2069402243070.2345475917020.7110760990270.9109428519011.790527186410.2924556443470.884286741231.1698797691-1.10448489195-0.285942705223-0.613165589489-2.04324017302-0.5611941441390.6436520888281.173803425350.3284372308140.06466917838520.6074377826710.2607262619740.76856499921812.84504967669.89221124326-39.3621042192
150.839431346874-0.5155558611251.066287004860.839471289085-0.8231450690991.06316108433-0.1527314705080.3099434099860.8820115379540.457249257838-0.254345481915-0.405881895453-1.27382721786-0.0597148836359-1.037431951541.24789387054-0.01175354283430.0868754233130.5055834045050.03740628358240.83233907554622.0225992656.0067951444-34.2296674431
160.478661797278-0.54360696482-0.2942850346720.299965476984-0.7103406737190.5278357111940.0202085036061-0.3028056617250.1542679785120.1231836588120.0621328942423-0.568720838598-0.5663556572210.6930594797420.0001531751584720.67453253565-0.022389847655-0.01652328417150.5935658916070.02914153451520.76035121348629.1193034461-7.24742160316-30.1241887529
172.31646356876-0.02259192920621.081524911820.5139512830340.1402245673241.94489244593-0.18823314043-1.355383155950.9599893953210.3251217550970.465656660398-0.0665581871331-0.70781850354-0.4007282840981.304957805610.8205145076290.1619692027060.05406437716810.5966739118710.010828778890.33152309138114.261766131-0.998850839498-25.1144766977
180.851339634907-0.0225494505494-0.3328068700180.673053131998-0.2586169987430.5564352374620.207471763852-0.342796451621-0.0713696159687-0.7186360049590.0664056199559-0.0788136281694-0.848321868306-0.8027410370540.1386153519931.032807437940.1864473834960.1245941883410.5139667172680.09673617671530.5649858565967.24830016257-1.30193815457-31.0752133524
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 94 through 173 )BB94 - 17394 - 173
22chain 'B' and (resid 174 through 189 )BB174 - 189174 - 189
33chain 'B' and (resid 190 through 212 )BB190 - 212190 - 212
44chain 'B' and (resid 213 through 240 )BB213 - 240213 - 240
55chain 'A' and (resid 1 through 13 )AA1 - 131 - 13
66chain 'A' and (resid 14 through 33 )AA14 - 3314 - 33
77chain 'A' and (resid 34 through 63 )AA34 - 6334 - 63
88chain 'A' and (resid 64 through 87 )AA64 - 8764 - 87
99chain 'A' and (resid 88 through 130 )AA88 - 13088 - 130
1010chain 'A' and (resid 131 through 151 )AA131 - 151131 - 151
1111chain 'A' and (resid 152 through 180 )AA152 - 180152 - 180
1212chain 'A' and (resid 181 through 202 )AA181 - 202181 - 202
1313chain 'A' and (resid 203 through 240 )AA203 - 240203 - 240
1414chain 'B' and (resid 1 through 13 )BB1 - 131 - 13
1515chain 'B' and (resid 14 through 33 )BB14 - 3314 - 33
1616chain 'B' and (resid 34 through 62 )BB34 - 6234 - 62
1717chain 'B' and (resid 63 through 79 )BB63 - 7963 - 79
1818chain 'B' and (resid 80 through 93 )BB80 - 9380 - 93

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