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- PDB-6ydb: Human wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP -

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Basic information

Entry
Database: PDB / ID: 6ydb
TitleHuman wtSTING in complex with 2',2'-difluoro-3',3'-c-di-GMP
ComponentsStimulator of interferon protein
KeywordsPROTEIN BINDING / innate immune system / cyclic dinucleotide / STING
Function / homology
Function and homology information


autophagosome membrane / positive regulation of type I interferon production / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of innate immune response / mitochondrial outer membrane / nucleotide binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm
Similarity search - Function
: / STING transmembrane domain / : / : / Stimulator of interferon genes protein / Stimulator of interferon genes protein, C-terminal domain superfamily / STING ligand-binding domain
Similarity search - Domain/homology
Chem-GGF / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.801 Å
AuthorsBoura, E. / Smola, M.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Ligand Strain and Its Conformational Complexity Is a Major Factor in the Binding of Cyclic Dinucleotides to STING Protein.
Authors: Smola, M. / Gutten, O. / Dejmek, M. / Kozisek, M. / Evangelidis, T. / Tehrani, Z.A. / Novotna, B. / Nencka, R. / Birkus, G. / Rulisek, L. / Boura, E.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8832
Polymers23,1891
Non-polymers6941
Water32418
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7674
Polymers46,3782
Non-polymers1,3892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4070 Å2
ΔGint-19 kcal/mol
Surface area14450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.073, 111.073, 35.836
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Stimulator of interferon protein


Mass: 23189.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STING, LOC340061, hCG_1782396 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-GGF / 2-azanyl-9-[(1~{R},6~{R},8~{R},9~{R},10~{R},15~{R},17~{R},18~{R})-17-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-9,18-bis(fluoranyl)-3,12-bis(oxidanyl)-3,12-bis(oxidanylidene)-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]-1~{H}-purin-6-one


Mass: 694.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22F2N10O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium chloride, 0.1 M Na/K phosphate pH 6.2, 40% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.801→39.275 Å / Num. obs: 5861 / % possible obs: 99.07 % / Redundancy: 15.7 % / CC1/2: 0.997 / CC star: 0.999 / Net I/σ(I): 9.71
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 561 / CC1/2: 0.581

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å39.06 Å
Translation5.36 Å39.06 Å

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSY

4ksy


Resolution: 2.801→39.2741 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.2454 293 5 %
Rwork0.2006 --
obs0.2028 5858 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.11 Å2 / Biso mean: 65.9723 Å2 / Biso min: 36.86 Å2
Refinement stepCycle: final / Resolution: 2.801→39.2741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1326 0 66 18 1410
Biso mean--53.49 54.76 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.801-3.52810.27191430.2422713
3.5281-39.27410.23471500.18642852

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