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- PDB-8hy9: Bacterial STING from Riemerella anatipestifer in complex with 3'3... -

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Basic information

Entry
Database: PDB / ID: 8hy9
TitleBacterial STING from Riemerella anatipestifer in complex with 3'3'-c-di-GMP
ComponentsCD-NTase-associated protein 12
KeywordsSIGNALING PROTEIN / CD-NTase-associated protein 12
Function / homologyChem-C2E / :
Function and homology information
Biological speciesRiemerella anatipestifer Yb2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.462 Å
AuthorsWang, Y.-C. / Yang, C.-S. / Hou, M.-H. / Chen, Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B241-001 Taiwan
Ministry of Science and Technology (MoST, Taiwan)111-2311-B-039-001-MY3 Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into the regulation, ligand recognition, and oligomerization of bacterial STING.
Authors: Hou, M.H. / Wang, Y.C. / Yang, C.S. / Liao, K.F. / Chang, J.W. / Shih, O. / Yeh, Y.Q. / Sriramoju, M.K. / Weng, T.W. / Jeng, U.S. / Hsu, S.D. / Chen, Y.
History
DepositionJan 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD-NTase-associated protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2943
Polymers18,5641
Non-polymers7302
Water2,234124
1
A: CD-NTase-associated protein 12
hetero molecules

A: CD-NTase-associated protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5896
Polymers37,1282
Non-polymers1,4614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4830 Å2
ΔGint-26 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.510, 40.990, 36.196
Angle α, β, γ (deg.)90.000, 105.041, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CD-NTase-associated protein 12 / NAD(+) hydrolase / TIR-STING


Mass: 18563.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: (1) The first four AA, SGGG, is a linker. (2) The fifth AA, PHE5, should be indexed as PHE158. Thank you very much!
Source: (gene. exp.) Riemerella anatipestifer Yb2 (bacteria)
Gene: KYF39_09390 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8F6THR5, NAD+ glycohydrolase
#2: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris pH 8.5, 0.2 M calcium chloride dihydrate, 40 % v/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.46→30 Å / Num. obs: 24248 / % possible obs: 99.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.227
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 2302 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBD

7ebd


Resolution: 1.462→22.805 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.272 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2095 1219 5.056 %
Rwork0.1813 22890 -
all0.183 --
obs-24109 98.328 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.222 Å2
Baniso -1Baniso -2Baniso -3
1-0.204 Å20 Å20.018 Å2
2---0.23 Å20 Å2
3---0.014 Å2
Refinement stepCycle: LAST / Resolution: 1.462→22.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 47 124 1457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0131362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171269
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6551859
X-RAY DIFFRACTIONr_angle_other_deg1.371.5872925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7285158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23424.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41715233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3155
X-RAY DIFFRACTIONr_chiral_restr0.0740.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined0.2270.2262
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.21141
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2661
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1620.217
X-RAY DIFFRACTIONr_nbd_other0.1810.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.236
X-RAY DIFFRACTIONr_mcbond_it1.7681.538635
X-RAY DIFFRACTIONr_mcbond_other1.761.537634
X-RAY DIFFRACTIONr_mcangle_it2.7012.304792
X-RAY DIFFRACTIONr_mcangle_other2.7032.306793
X-RAY DIFFRACTIONr_scbond_it2.9541.882727
X-RAY DIFFRACTIONr_scbond_other2.9581.884725
X-RAY DIFFRACTIONr_scangle_it4.4752.6791067
X-RAY DIFFRACTIONr_scangle_other4.4732.6781068
X-RAY DIFFRACTIONr_lrange_it5.78619.4291546
X-RAY DIFFRACTIONr_lrange_other5.73619.2191528
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.462-1.50.285700.311383X-RAY DIFFRACTION82.1833
1.5-1.5410.318780.2411649X-RAY DIFFRACTION98.7986
1.541-1.5850.224970.2081632X-RAY DIFFRACTION99.9422
1.585-1.6340.2011040.1831544X-RAY DIFFRACTION100
1.634-1.6870.214770.1861520X-RAY DIFFRACTION100
1.687-1.7470.223610.1681480X-RAY DIFFRACTION100
1.747-1.8120.181760.1711451X-RAY DIFFRACTION100
1.812-1.8860.209740.1681369X-RAY DIFFRACTION99.8616
1.886-1.9690.164740.1661295X-RAY DIFFRACTION99.927
1.969-2.0650.18790.1621251X-RAY DIFFRACTION100
2.065-2.1760.181690.1611201X-RAY DIFFRACTION99.8428
2.176-2.3080.186680.1551117X-RAY DIFFRACTION98.9975
2.308-2.4660.178480.1611081X-RAY DIFFRACTION99.0351
2.466-2.6620.177380.176969X-RAY DIFFRACTION97.862
2.662-2.9140.208480.182931X-RAY DIFFRACTION100
2.914-3.2540.248430.193845X-RAY DIFFRACTION100
3.254-3.750.221340.178752X-RAY DIFFRACTION100
3.75-4.5750.168350.172639X-RAY DIFFRACTION99.41
4.575-6.3960.367300.214490X-RAY DIFFRACTION100
6.396-22.8050.207160.205291X-RAY DIFFRACTION97.4603

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