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- PDB-5yf7: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 5yf7
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-672)
ComponentsRdRp catalytic
KeywordsTRANSFERASE
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing ...serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity / viral protein processing / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / proteolysis / RNA binding / ATP binding / membrane / cytoplasm
Similarity search - Function
Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 ...Pestivirus envelope glycoprotein E2, domain A / Pestivirus envelope glycoprotein E2, domain B / Capsid protein C, pestivirus / Pestivirus nonstructural protein 2 / Pestivirus NS2, peptidase C74 / Capsid protein C, pestivirus / Pestivirus NS2 peptidase / Pestivirus nonstructural protein 2 (NS2) protease domain profile. / Pestivirus NS3, peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus envelope glycoprotein E2, domain D / Pestivirus NS3 polyprotein peptidase S31 / Pestivirus envelope glycoprotein E2 / Pestivirus NS3 protease (NS3pro) domain profile. / Peptidase C53, pestivirus Npro, interaction domain / Peptidase C53, pestivirus Npro / Pestivirus Npro endopeptidase C53 / Pestivirus N-terminal protease Npro domain profile. / Ribonuclease T2, His active site 2 / Ribonuclease T2 family histidine active site 2. / Ribonuclease T2-like superfamily / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / : / Flavivirus NS3 helicase, C-terminal helical domain / DEAD box, Flavivirus / Flavivirus DEAD domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsLiu, W. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670154 China
National Key Basic Research Program of China2013CB911100 China
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: A unique intra-molecular fidelity-modulating mechanism identified in a viral RNA-dependent RNA polymerase.
Authors: Liu, W. / Shi, X. / Gong, P.
History
DepositionSep 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RdRp catalytic


Theoretical massNumber of molelcules
Total (without water)78,1561
Polymers78,1561
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28100 Å2
Unit cell
Length a, b, c (Å)162.249, 162.249, 56.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RdRp catalytic


Mass: 78156.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Variant: T690A / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5U8X5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.39 Å3/Da / Density % sol: 48.6 % / Mosaicity: 0.339 °
Crystal growTemperature: 289 K / Method: evaporation / pH: 8 / Details: Polypropylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 35366 / % possible obs: 99.2 % / Redundancy: 12.7 % / Biso Wilson estimate: 42.48 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.021 / Rrim(I) all: 0.078 / Χ2: 0.957 / Net I/σ(I): 6.4 / Num. measured all: 450669
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.27-2.3512.40.4934160.9680.1380.510.93298.3
2.35-2.4512.80.40634880.9750.1140.4220.92799.8
2.45-2.5612.30.30934930.9830.0880.3220.95299.8
2.56-2.69130.2435160.990.0670.2490.95299.7
2.69-2.8613.30.17235100.9940.0480.1790.97599.7
2.86-3.0812.80.1235250.9960.0340.1250.96799.8
3.08-3.3912.80.08835230.9970.0240.0911.01498.9
3.39-3.8813.10.06635680.9980.0180.0680.97899.4
3.88-4.8912.70.05335830.9990.0150.0550.92198.9
4.89-5012.10.04337440.9990.0130.0450.9597.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJQ

2cjq


Resolution: 2.27→39.351 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2453 1745 4.95 %
Rwork0.1988 33514 -
obs0.2011 35259 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.46 Å2 / Biso mean: 52.1765 Å2 / Biso min: 26.2 Å2
Refinement stepCycle: final / Resolution: 2.27→39.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5124 0 0 211 5335
Biso mean---47.6 -
Num. residues----650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075237
X-RAY DIFFRACTIONf_angle_d0.8267083
X-RAY DIFFRACTIONf_chiral_restr0.047781
X-RAY DIFFRACTIONf_plane_restr0.005902
X-RAY DIFFRACTIONf_dihedral_angle_d9.5843150
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2701-2.33690.32841410.25912633277496
2.3369-2.41230.31731320.25212782291499
2.4123-2.49850.32941810.244427482929100
2.4985-2.59850.29421530.236327602913100
2.5985-2.71670.28561170.236628212938100
2.7167-2.85990.33251500.242627752925100
2.8599-3.03910.31241470.234427882935100
3.0391-3.27360.27381320.22722790292299
3.2736-3.60280.23391570.20942811296899
3.6028-4.12370.23451480.17982816296499
4.1237-5.19350.19431390.15962862300199
5.1935-39.35710.19771480.17012928307696

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