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- PDB-5yf6: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 5yf6
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-682)
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: 2.1 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)79,3991
Polymers79,3991
Non-polymers00
Water6,197344
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 area28070 Å2
Unit cell
Length a, b, c (Å)161.352, 161.352, 55.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-735-

HOH

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Components

#1: Protein RdRp catalytic


Mass: 79398.883 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.: 344 / 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: 2.29 Å3/Da / Density % sol: 46.38 % / Mosaicity: 0.47 °
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: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43794 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 35.61 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.022 / Rrim(I) all: 0.07 / Χ2: 1.032 / Net I/σ(I): 11.9 / Num. measured all: 448970
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1810.30.45942970.9550.150.4831.009100
2.18-2.2610.40.34742950.9710.1130.3661.055100
2.26-2.3710.40.26842870.9850.0870.2821.092100
2.37-2.4910.50.243470.990.0650.211.071100
2.49-2.6510.50.14743400.9950.0480.1551.069100
2.65-2.8510.50.10343390.9970.0330.1081.091100
2.85-3.1410.50.06843720.9980.0220.0710.981100
3.14-3.5910.30.05843900.9980.0190.0611.007100
3.59-4.529.60.05444520.9980.0190.0580.951100
4.52-509.50.03746750.9990.0130.040.9999.7

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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: 2.1→45.987 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.227 2188 5.01 %
Rwork0.1796 41491 -
obs0.1819 43679 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.7 Å2 / Biso mean: 40.2835 Å2 / Biso min: 21.21 Å2
Refinement stepCycle: final / Resolution: 2.1→45.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5108 0 0 344 5452
Biso mean---41.58 -
Num. residues----646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075218
X-RAY DIFFRACTIONf_angle_d0.87052
X-RAY DIFFRACTIONf_chiral_restr0.048778
X-RAY DIFFRACTIONf_plane_restr0.005898
X-RAY DIFFRACTIONf_dihedral_angle_d9.9823146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1001-2.14570.28761260.20625472673100
2.1457-2.19560.31121300.203625552685100
2.1956-2.25050.2591300.198525682698100
2.2505-2.31140.2751690.197425202689100
2.3114-2.37940.25351290.195325482677100
2.3794-2.45620.25041310.193825712702100
2.4562-2.5440.27621440.186125632707100
2.544-2.64580.2271440.1925552699100
2.6458-2.76620.24581300.188625682698100
2.7662-2.9120.22441220.195325952717100
2.912-3.09450.2371330.19326012734100
3.0945-3.33330.23921530.193225772730100
3.3333-3.66860.26731400.181226042744100
3.6686-4.19920.17181400.158426302770100
4.1992-5.28930.18451360.150426712807100
5.2893-45.99780.21511310.18112818294999

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