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- PDB-6ae7: Crystals structure of Classical swine fever virus NS5B (residues ... -

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Basic information

Entry
Database: PDB / ID: 6ae7
TitleCrystals structure of Classical swine fever virus NS5B (residues 1-672, E472A mutant)
ComponentsRdRp catalytic
KeywordsTRANSFERASE / Polymerase
Function / homology
Function and homology information


serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / host cell cytoplasm / RNA helicase activity ...serine-type exopeptidase activity / ribonuclease T2 activity / host cell membrane / ribonucleoside triphosphate phosphatase activity / : / protein complex oligomerization / monoatomic ion channel activity / 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 / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / 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
ACETATE ION / Genome polyprotein
Similarity search - Component
Biological speciesClassical swine fever virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLiu, W. / Gong, P.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670154 China
Ministry of Science and Technology (China)2018YFA0507200 China
Ministry of Science and Technology (China)2018YFD0500100 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
DepositionAug 3, 2018Deposition 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,2764
Polymers78,0981
Non-polymers1773
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-1 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.892, 116.892, 394.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein RdRp catalytic


Mass: 78098.383 Da / Num. of mol.: 1 / Mutation: E472A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Classical swine fever virus / Strain: Shimen / Gene: NS5B / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5U8X5
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2

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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: 4.32 Å3/Da / Density % sol: 71.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: SOKALAN CP42

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 14040 / % possible obs: 99.8 % / Redundancy: 11.2 % / Biso Wilson estimate: 88.14 Å2 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.045 / Rrim(I) all: 0.151 / Χ2: 1.078 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.8-3.9411.60.50313640.9870.1530.5261.08499.9
3.94-4.0911.60.37113750.9930.1140.3881.0899.9
4.09-4.2811.50.32713640.9920.1010.3431.07699.9
4.28-4.511.40.2213920.9930.0690.2311.118100
4.5-4.7911.40.21113730.9960.0650.2211.07899.9
4.79-5.1611.30.20513950.9940.0640.2151.07199.9
5.16-5.6711.30.18114020.9950.0560.191.0899.8
5.67-6.4910.90.14714220.9950.0470.1551.09299.9
6.49-8.1811.20.0914290.9970.0280.0941.03899.9
8.18-509.70.04715240.9990.0160.051.06798.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJQ

2cjq


Resolution: 3.8→40.451 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.01
RfactorNum. reflection% reflection
Rfree0.2459 721 5.18 %
Rwork0.2118 --
obs0.2135 13913 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.75 Å2 / Biso mean: 104.6501 Å2 / Biso min: 59.73 Å2
Refinement stepCycle: final / Resolution: 3.8→40.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4807 0 12 0 4819
Biso mean--94.13 --
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034925
X-RAY DIFFRACTIONf_angle_d0.5896708
X-RAY DIFFRACTIONf_chiral_restr0.042761
X-RAY DIFFRACTIONf_plane_restr0.006866
X-RAY DIFFRACTIONf_dihedral_angle_d7.1732899
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.8001-4.09320.25431280.23252558268698
4.0932-4.50460.23861480.21872585273399
4.5046-5.15530.25491320.21132613274599
5.1553-6.49080.26951460.234426652811100
6.4908-40.45370.23211670.191327712938100

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