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- PDB-9fej: Structure of the RNA-dependent RNA polymerase P2 from the bacteri... -

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Basic information

Entry
Database: PDB / ID: 9fej
TitleStructure of the RNA-dependent RNA polymerase P2 from the bacteriophage Phi8
ComponentsRNA-directed RNA polymerase
KeywordsVIRAL PROTEIN / polymerase
Function / homologyCystovirus, RNA-directed RNA polymerase / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / RNA-directed RNA polymerase / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA/RNA polymerase superfamily / metal ion binding / RNA-directed RNA polymerase
Function and homology information
Biological speciesPseudomonas phage phi8 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLatimer-Smith, M. / Salgado, P.S. / Forsyth, I. / Makeyev, E. / Poranen, M. / Stuart, D.I. / Grimes, J.M. / El Omari, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2024
Title: Structure of the RNA-dependent RNA polymerase P2 from the cystovirus phi 8.
Authors: Latimer-Smith, M. / Salgado, P.S. / Forsyth, I. / Makeyev, E. / Poranen, M.M. / Stuart, D.I. / Grimes, J.M. / El Omari, K.
History
DepositionMay 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7532
Polymers71,7131
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.666, 96.666, 267.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein RNA-directed RNA polymerase


Mass: 71712.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage phi8 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9MC15, RNA-directed RNA polymerase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
Has protein modificationN

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 140 mM CaCl2, 14% PEG 3350, 100 mM Tris pH 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 6, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 3→267.47 Å / Num. obs: 15667 / % possible obs: 100 % / Redundancy: 40.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.04 / Rrim(I) all: 0.254 / Net I/σ(I): 5.6 / Num. measured all: 635295
Reflection shellResolution: 3→3.05 Å / % possible obs: 96.4 % / Redundancy: 30.7 % / Rmerge(I) obs: 2.596 / Num. measured all: 22492 / Num. unique obs: 732 / CC1/2: 0.575 / Rpim(I) all: 0.462 / Rrim(I) all: 2.641 / Net I/σ(I) obs: 0.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→83.71 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 800 5.37 %
Rwork0.2543 --
obs0.2558 14897 95.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→83.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5034 0 1 0 5035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.429
X-RAY DIFFRACTIONf_dihedral_angle_d11.3791913
X-RAY DIFFRACTIONf_chiral_restr0.036743
X-RAY DIFFRACTIONf_plane_restr0.003899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.37261020.38511694X-RAY DIFFRACTION71
3.19-3.430.34371340.33912404X-RAY DIFFRACTION100
3.44-3.780.28271400.29662402X-RAY DIFFRACTION100
3.78-4.330.31041310.2612438X-RAY DIFFRACTION100
4.33-5.450.26251390.22592495X-RAY DIFFRACTION100
5.45-83.710.24841540.20882664X-RAY DIFFRACTION100

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