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- PDB-8hy8: Bacterial STING from Epilithonimonas lactis -

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Basic information

Entry
Database: PDB / ID: 8hy8
TitleBacterial STING from Epilithonimonas lactis
ComponentsCD-NTase-associated protein 12
KeywordsSIGNALING PROTEIN / CD-NTase-associated protein 12
Function / homologyCD-NTase-associated protein 12/Pycsar effector protein, TIR domain / CAP12/Pycsar effector protein, TIR domain / Prokaryotic STING domain / Prokaryotic STING domain / NAD+ glycohydrolase / NADP+ nucleosidase activity / defense response to virus / nucleotide binding / CD-NTase-associated protein 12
Function and homology information
Biological speciesEpilithonimonas lactis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.568 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


Theoretical massNumber of molelcules
Total (without water)18,8141
Polymers18,8141
Non-polymers00
Water73941
1
A: CD-NTase-associated protein 12

A: CD-NTase-associated protein 12


Theoretical massNumber of molelcules
Total (without water)37,6272
Polymers37,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area1830 Å2
ΔGint-21 kcal/mol
Surface area16910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.981, 56.981, 187.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-239-

HOH

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Components

#1: Protein CD-NTase-associated protein 12


Mass: 18813.592 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The GLU5 should be re-indexed as GLU152. Thank you very much!
Source: (gene. exp.) Epilithonimonas lactis (bacteria) / Gene: IO89_10965 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A085BE66
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: 47.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MOPSO/Bis-Tris pH 7.5, 90 mM lithium/sodium/potassium sulfate, 15 % (w/v) PEG 3000, 20 % (v/v) 1, 2, 4-Butanetriol, 1 % (w/v) NDSB 256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.56→30 Å / Num. obs: 6344 / % possible obs: 99.2 % / Redundancy: 18.8 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 20.5
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 1.43 / Num. unique obs: 572 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
MOLREP11.7.03phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EBL

7ebl


Resolution: 2.568→23.873 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.903 / SU B: 9.867 / SU ML: 0.207 / Cross valid method: THROUGHOUT / ESU R: 0.873 / ESU R Free: 0.311
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.244 290 4.908 %
Rwork0.2073 5619 -
all0.209 --
obs-5909 93.158 %
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: 40.987 Å2
Baniso -1Baniso -2Baniso -3
1--0.101 Å2-0.05 Å2-0 Å2
2---0.101 Å20 Å2
3---0.326 Å2
Refinement stepCycle: LAST / Resolution: 2.568→23.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1235 0 0 41 1276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131254
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171235
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.6411692
X-RAY DIFFRACTIONr_angle_other_deg1.1891.5832849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5435151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.27424.67762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.29315241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.323154
X-RAY DIFFRACTIONr_chiral_restr0.0580.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021390
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02266
X-RAY DIFFRACTIONr_nbd_refined0.2070.2239
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21086
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2590
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2627
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1320.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1830.26
X-RAY DIFFRACTIONr_nbd_other0.2010.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.240.24
X-RAY DIFFRACTIONr_mcbond_it4.0793.94610
X-RAY DIFFRACTIONr_mcbond_other4.0733.938609
X-RAY DIFFRACTIONr_mcangle_it6.4975.882759
X-RAY DIFFRACTIONr_mcangle_other6.4945.884760
X-RAY DIFFRACTIONr_scbond_it4.4514.621644
X-RAY DIFFRACTIONr_scbond_other4.4474.621641
X-RAY DIFFRACTIONr_scangle_it7.4346.672933
X-RAY DIFFRACTIONr_scangle_other7.4326.671932
X-RAY DIFFRACTIONr_lrange_it10.65544.681325
X-RAY DIFFRACTIONr_lrange_other10.65344.6961326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.568-2.6340.43270.307218X-RAY DIFFRACTION50.1114
2.634-2.7060.237130.276284X-RAY DIFFRACTION66.7416
2.706-2.7840.198170.276367X-RAY DIFFRACTION94.1176
2.784-2.8690.334210.264387X-RAY DIFFRACTION96.4539
2.869-2.9620.369260.235373X-RAY DIFFRACTION100
2.962-3.0650.392160.218370X-RAY DIFFRACTION100
3.065-3.1790.194200.248373X-RAY DIFFRACTION100
3.179-3.3080.24240.188334X-RAY DIFFRACTION100
3.308-3.4530.127120.207331X-RAY DIFFRACTION100
3.453-3.6190.228130.188336X-RAY DIFFRACTION100
3.619-3.8110.289140.169313X-RAY DIFFRACTION99.6951
3.811-4.0390.232180.177282X-RAY DIFFRACTION99.3378
4.039-4.3120.205190.157275X-RAY DIFFRACTION99.661
4.312-4.6490.124130.164262X-RAY DIFFRACTION99.6377
4.649-5.0810.243190.186244X-RAY DIFFRACTION100
5.081-5.660.226110.251230X-RAY DIFFRACTION100
5.66-6.4980.29590.26202X-RAY DIFFRACTION99.5283
6.498-7.8660.7170.236186X-RAY DIFFRACTION99.4845
7.866-10.7610.22680.18149X-RAY DIFFRACTION99.3671
10.761-23.8730.06830.23103X-RAY DIFFRACTION92.1739

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