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- PDB-5mus: Structure of the C-terminal domain of a reptarenavirus L protein -

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Basic information

Entry
Database: PDB / ID: 5mus
TitleStructure of the C-terminal domain of a reptarenavirus L protein
ComponentsL protein
KeywordsVIRAL PROTEIN / Arenavirus / polymerase / putative cap-binding
Function / homology
Function and homology information


cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
RNA polymerase, arenaviral / RNA endonuclease, cap-snatching / Arenavirus RNA polymerase / Arenavirus cap snatching domain / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesCAS virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.009 Å
AuthorsRosenthal, M. / Gogrefe, N. / Reguera, J. / Vogel, D. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
DFGRE 3712/1-1 Germany
DFGGU 883/1-1 Germany
DFGGU 883/4-1 Germany
CitationJournal: PLoS Pathog. / Year: 2017
Title: Structural insights into reptarenavirus cap-snatching machinery.
Authors: Rosenthal, M. / Gogrefe, N. / Vogel, D. / Reguera, J. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
History
DepositionJan 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L protein
B: L protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3746
Polymers75,0622
Non-polymers3124
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6970 Å2
ΔGint-22 kcal/mol
Surface area31280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.392, 76.942, 116.920
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 L protein


Mass: 37531.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAS virus / Production host: Escherichia coli (E. coli) / References: UniProt: J7HBG8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 37% Jeffamine ED-2001, 2 mM TCEP and 100 mM HEPES pH 7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.009→63.95 Å / Num. obs: 45942 / % possible obs: 98 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.04953 / Rrim(I) all: 0.07005 / Net I/σ(I): 8.36
Reflection shellResolution: 2.009→2.081 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.51 / Num. unique obs: 4525 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLM7.1.3data reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.009→63.95 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 2320 5.05 %
Rwork0.1976 --
obs0.1999 45931 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.009→63.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5238 0 19 384 5641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085365
X-RAY DIFFRACTIONf_angle_d0.9277248
X-RAY DIFFRACTIONf_dihedral_angle_d14.3213282
X-RAY DIFFRACTIONf_chiral_restr0.052825
X-RAY DIFFRACTIONf_plane_restr0.006921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.009-2.050.36981420.31742518X-RAY DIFFRACTION99
2.05-2.09460.31791230.29452529X-RAY DIFFRACTION98
2.0946-2.14330.35091060.26192570X-RAY DIFFRACTION99
2.1433-2.19690.27191320.24182543X-RAY DIFFRACTION99
2.1969-2.25630.27891280.23612584X-RAY DIFFRACTION99
2.2563-2.32270.28261270.22072550X-RAY DIFFRACTION99
2.3227-2.39770.2681570.20382531X-RAY DIFFRACTION99
2.3977-2.48340.26711530.20632556X-RAY DIFFRACTION99
2.4834-2.58280.26851400.2022553X-RAY DIFFRACTION99
2.5828-2.70040.22131220.19752568X-RAY DIFFRACTION99
2.7004-2.84280.26231520.19632571X-RAY DIFFRACTION99
2.8428-3.02090.29251670.19252516X-RAY DIFFRACTION99
3.0209-3.25410.23911120.18212597X-RAY DIFFRACTION98
3.2541-3.58160.20151320.17082586X-RAY DIFFRACTION98
3.5816-4.09970.21481620.16482552X-RAY DIFFRACTION98
4.0997-5.16490.20831190.16362628X-RAY DIFFRACTION97
5.1649-63.98390.22141460.22162659X-RAY DIFFRACTION96

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