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- PDB-7sbi: Tandem diubiquitin-like domain from chicken 2'-5'-oligoadenylate ... -

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Basic information

Entry
Database: PDB / ID: 7sbi
TitleTandem diubiquitin-like domain from chicken 2'-5'-oligoadenylate synthetase-like protein
Components2'-5' oligoadenylate synthase
KeywordsIMMUNE SYSTEM / Ubiquitin-like / Oligoadenylate synthetase-like
Function / homology
Function and homology information


2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / double-stranded RNA binding / defense response to virus / innate immune response / cytoplasm
Similarity search - Function
2'-5'-oligoadenylate synthase / 2-5-oligoadenylate synthetase, C-terminal conserved site / 2'-5'-oligoadenylate synthetase 1, domain 2/C-terminal / 2'-5'-oligoadenylate synthases signature 2. / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / Ubiquitin-like domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily ...2'-5'-oligoadenylate synthase / 2-5-oligoadenylate synthetase, C-terminal conserved site / 2'-5'-oligoadenylate synthetase 1, domain 2/C-terminal / 2'-5'-oligoadenylate synthases signature 2. / 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus / Ubiquitin-like domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Nucleotidyltransferase superfamily / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
2'-5' oligoadenylate synthase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsFreitas, B.T. / Pegan, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Front Immunol / Year: 2022
Title: The Structure and Immune Regulatory Implications of the Ubiquitin-Like Tandem Domain Within an Avian 2'-5' Oligoadenylate Synthetase-Like Protein
Authors: Shepard, J.D. / Freitas, B.T. / Rodriguez, S.E. / Scholte, F.E.M. / Baker, K. / Hutchison, M.R. / Longo, J.E. / Miller, H.C. / O'Boyle, B.M. / Tandon, A. / Zhao, P. / Grimsey, N.J. / Wells, ...Authors: Shepard, J.D. / Freitas, B.T. / Rodriguez, S.E. / Scholte, F.E.M. / Baker, K. / Hutchison, M.R. / Longo, J.E. / Miller, H.C. / O'Boyle, B.M. / Tandon, A. / Zhao, P. / Grimsey, N.J. / Wells, L. / Bergeron, E. / Pegan, S.D.
History
DepositionSep 24, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Apr 10, 2024Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2'-5' oligoadenylate synthase
B: 2'-5' oligoadenylate synthase


Theoretical massNumber of molelcules
Total (without water)37,1672
Polymers37,1672
Non-polymers00
Water1,04558
1
A: 2'-5' oligoadenylate synthase


Theoretical massNumber of molelcules
Total (without water)18,5831
Polymers18,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2'-5' oligoadenylate synthase


Theoretical massNumber of molelcules
Total (without water)18,5831
Polymers18,5831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.921, 100.922, 55.748
Angle α, β, γ (deg.)90.000, 104.962, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 348 through 364 or resid 366...
d_2ens_1(chain "B" and (resid 348 through 364 or resid 366...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1HISARGA1 - 17
d_12ens_1VALVALA19 - 86
d_13ens_1ASPGLNA88 - 121
d_14ens_1LEUTHRA123 - 127
d_15ens_1GLUPROA129 - 143
d_16ens_1SERARGA145 - 154
d_21ens_1HISARGB2 - 18
d_22ens_1VALASNB20 - 53
d_23ens_1PROVALB55 - 88
d_24ens_1ASPGLNB90 - 123
d_25ens_1LEUTHRB125 - 129
d_26ens_1GLUPROB131 - 145
d_27ens_1SERARGB147 - 156

NCS oper: (Code: givenMatrix: (-0.999996128673, -0.000965429681538, 0.00260970978766), (0.000959782639856, -0.999997197426, -0.00216424510234), (0.00261179190022, -0.00216173196969, 0.999994252712) ...NCS oper: (Code: given
Matrix: (-0.999996128673, -0.000965429681538, 0.00260970978766), (0.000959782639856, -0.999997197426, -0.00216424510234), (0.00261179190022, -0.00216173196969, 0.999994252712)
Vector: 58.6052033844, -48.7937515403, -0.109728903638)

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Components

#1: Protein 2'-5' oligoadenylate synthase


Mass: 18583.332 Da / Num. of mol.: 2 / Fragment: UBL domain (UNP residues 348-503)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: OAS*A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O13255
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: tri-ammonium citrate, PEG 3350, galactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→28.53 Å / Num. obs: 13956 / % possible obs: 93.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 40.39 Å2 / Rpim(I) all: 0.075 / Net I/σ(I): 8.3
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1176 / CC1/2: 0.993 / Rpim(I) all: 1.1 / % possible all: 79.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXphasing
PHENIXphenix-1.18.2-3874refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology Model

Resolution: 2.23→27.94 Å / SU ML: 0.3978 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 31.7325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.255 700 5.02 %
Rwork0.2294 13238 -
obs0.2307 13938 93.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.78 Å2
Refinement stepCycle: LAST / Resolution: 2.23→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 58 2601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00192591
X-RAY DIFFRACTIONf_angle_d0.54953511
X-RAY DIFFRACTIONf_chiral_restr0.0411409
X-RAY DIFFRACTIONf_plane_restr0.0044442
X-RAY DIFFRACTIONf_dihedral_angle_d21.6867988
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.673492414469 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.410.38961370.33722458X-RAY DIFFRACTION87.2
2.41-2.650.29741400.29112703X-RAY DIFFRACTION94.58
2.65-3.030.29821490.27092665X-RAY DIFFRACTION95.78
3.03-3.820.29181330.23462694X-RAY DIFFRACTION93.76
3.82-27.940.18831410.18332718X-RAY DIFFRACTION93.98

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