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- PDB-6ywb: Human wtSTING in complex with 3',3'-c-[2'FdAMP-2'FdAM(PS)] -

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Basic information

Entry
Database: PDB / ID: 6ywb
TitleHuman wtSTING in complex with 3',3'-c-[2'FdAMP-2'FdAM(PS)]
ComponentsStimulator of interferon protein
KeywordsPROTEIN BINDING / Innate immune system / CDN / agonist
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
3',3'-c-[2'FdAMP-2'FdAM(PS)] / Stimulator of interferon genes protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.503 Å
AuthorsBoura, E. / Smola, M.
CitationJournal: To Be Published
Title: Human wtSTING in complex with 3',3'-c-[2'FdAMP-2'FdAM(PS)]
Authors: Boura, E. / Smola, M.
History
DepositionApr 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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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)23,8702
Polymers23,1891
Non-polymers6801
Water64936
1
A: Stimulator of interferon protein
hetero molecules

A: Stimulator of interferon protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7394
Polymers46,3782
Non-polymers1,3612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Unit cell
Length a, b, c (Å)110.906, 110.906, 35.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-532-

HOH

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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 (E. coli) / References: UniProt: A0A2R3XZB7
#2: Chemical ChemComp-PWB / 3',3'-c-[2'FdAMP-2'FdAM(PS)] / 9-[(1~{R},6~{R},8~{R},9~{R},10~{R},12~{R},15~{R},17~{R},18~{R})-17-(6-aminopurin-9-yl)-9,18-bis(fluoranyl)-3-oxidanyl-3,12-bis(oxidanylidene)-12-sulfanyl-2,4,7,11,13,16-hexaoxa-3$l^{5},12$l^{5}-diphosphatricyclo[13.3.0.0^{6,10}]octadecan-8-yl]purin-6-amine


Mass: 680.475 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24F2N10O9P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.37 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Sodium/Potassium tartrate, 0.2 M Lithium sulfate, 0.1 M Tris pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.503→35.07 Å / Num. obs: 8087 / % possible obs: 99.54 % / Redundancy: 8.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.1618 / Rpim(I) all: 0.0599 / Net I/σ(I): 10.69
Reflection shellResolution: 2.503→2.593 Å / Rmerge(I) obs: 1.031 / Num. unique obs: 769 / CC1/2: 0.729 / Rpim(I) all: 0.3707

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KSY

4ksy


Resolution: 2.503→35.07 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.77
RfactorNum. reflection% reflection
Rfree0.2563 404 5 %
Rwork0.2095 --
obs0.2117 8085 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 94.24 Å2 / Biso mean: 42.8952 Å2 / Biso min: 14.8 Å2
Refinement stepCycle: final / Resolution: 2.503→35.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 44 36 1424
Biso mean--28.97 41.29 -
Num. residues----171
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5034-2.86560.25261310.2441248199
2.8656-3.60990.31291320.22352529100
3.6099-35.070.23141410.19352671100

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