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- PDB-1px5: Crystal structure of the 2'-specific and double-stranded RNA-acti... -

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Basic information

Entry
Database: PDB / ID: 1px5
TitleCrystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase
Components2'-5'-oligoadenylate synthetase 1
KeywordsTRANSFERASE / 5-stranded antiparalel beta sheet / four helix bundle
Function / homology
Function and homology information


negative regulation of transformation of host cell by virus / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / negative regulation of viral genome replication / double-stranded RNA binding / defense response to virus / innate immune response / endoplasmic reticulum / mitochondrion ...negative regulation of transformation of host cell by virus / 2'-5' oligoadenylate synthase / 2'-5'-oligoadenylate synthetase activity / regulation of ribonuclease activity / negative regulation of viral genome replication / double-stranded RNA binding / defense response to virus / innate immune response / endoplasmic reticulum / mitochondrion / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / cytoplasm / cytosol
Similarity search - Function
2'-5'-oligoadenylate synthetase 1, domain 2 / 2-5-oligoadenylate synthetase, N-terminal conserved site / 2'-5'-oligoadenylate synthases signature 1. / 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 / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain ...2'-5'-oligoadenylate synthetase 1, domain 2 / 2-5-oligoadenylate synthetase, N-terminal conserved site / 2'-5'-oligoadenylate synthases signature 1. / 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 / 2'-5'-oligoadenylate synthase N-terminal region profile. / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-5'-oligoadenylate synthase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.74 Å
AuthorsHartmann, R. / Justesen, J. / Sarkar, S.N. / Sen, G.C. / Yee, V.C.
CitationJournal: Mol.Cell / Year: 2003
Title: Crystal structure of the 2'-specific and double-stranded RNA-activated interferon-induced antiviral protein 2'-5'-oligoadenylate synthetase
Authors: Hartmann, R. / Justesen, J. / Sarkar, S.N. / Sen, G.C. / Yee, V.C.
History
DepositionJul 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2'-5'-oligoadenylate synthetase 1
B: 2'-5'-oligoadenylate synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2236
Polymers80,8392
Non-polymers3844
Water13,872770
1
A: 2'-5'-oligoadenylate synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6123
Polymers40,4191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2'-5'-oligoadenylate synthetase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6123
Polymers40,4191
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.524, 132.601, 57.305
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 2'-5'-oligoadenylate synthetase 1 / (2-5')oligo(A)synthetase 1 / 2-5A synthetase 1 / p42 OAS


Mass: 40419.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OAS1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: Q29599, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 770 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 2000mme, sodium cacodylate, ammonium sulfate, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlprotein1drop
230 %PEG2000 MME1reservoir
30.2 Mammonium sulfate1reservoir
40.1 Msodium cacodylate1reservoirpH6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.74→19.95 Å / Num. all: 70008 / Num. obs: 69379 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 32.4
Reflection shellResolution: 1.74→1.8 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.1 / % possible all: 96.7
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 99.4 % / Redundancy: 6.1 %
Reflection shell
*PLUS
% possible obs: 96.7 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 7.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.74→19.95 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4925 7.1 %RANDOM
Rwork0.187 ---
obs0.187 69379 99.2 %-
all-70008 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.6205 Å2 / ksol: 0.353352 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.54 Å20 Å23.51 Å2
2---2.5 Å20 Å2
3----5.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.74→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5460 0 20 770 6250
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it2.293
X-RAY DIFFRACTIONc_mcangle_it3.213.5
X-RAY DIFFRACTIONc_scbond_it3.323.5
X-RAY DIFFRACTIONc_scangle_it4.854
LS refinement shellResolution: 1.74→1.85 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 820 7.3 %
Rwork0.224 10408 -
obs-10408 96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_MOD.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.2242 / Rfactor Rwork: 0.1868
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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