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- PDB-6gp9: Structural studies of hepatitis C virus non-structural protein-5b... -

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Basic information

Entry
Database: PDB / ID: 6gp9
TitleStructural studies of hepatitis C virus non-structural protein-5b of genotype 4a
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / Hepatitic C virus / Genotype 4a / non structural 5 b (NS5b) protein
Function / homology
Function and homology information


host cell membrane / peptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / nucleotide binding / fusion of virus membrane with host endosome membrane / ATP hydrolysis activity / proteolysis / RNA binding / membrane
Similarity search - Function
RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA-directed RNA polymerase
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsJanowski, R. / Geber, H. / Protzer, U. / Niessing, D.
CitationJournal: Biorxiv / Year: 2022
Title: Structural studies of hepatitis C virus non-structural protein-5b of genotype 4a
Authors: Gaber, H. / Niessing, D. / Protzer, U. / Janowski, R.
History
DepositionJun 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)64,0511
Polymers64,0511
Non-polymers00
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 87.050, 96.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-directed RNA polymerase


Mass: 64050.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Production host: Escherichia coli (E. coli) / References: UniProt: Q506M7, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 100 mM sodium citrate pH 5.4, 25-30% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. obs: 10145 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 77.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.138 / Net I/σ(I): 9.23
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.74 / Num. unique obs: 742 / CC1/2: 0.713 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C2P

1c2p


Resolution: 3.1→64.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.897 / SU B: 27.846 / SU ML: 0.453 / Cross valid method: THROUGHOUT / ESU R Free: 0.545
RfactorNum. reflection% reflectionSelection details
Rfree0.25735 509 5 %RANDOM
Rwork0.20183 ---
obs0.20462 9635 99.71 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 70 Å2
Baniso -1Baniso -2Baniso -3
1--6.75 Å2-0 Å2-0 Å2
2--2.5 Å20 Å2
3---4.25 Å2
Refinement stepCycle: 1 / Resolution: 3.1→64.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 0 16 4340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194424
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9616010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8445552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26422.21181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.37915749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6121540
X-RAY DIFFRACTIONr_chiral_restr0.1160.2684
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213305
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.5447.5252211
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.19811.292762
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.5367.8452213
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined13.68819004
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.181 Å
RfactorNum. reflection% reflection
Rfree0.33 45 -
Rwork0.35 695 -
obs--100 %

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