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

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Basic information

Entry
Database: PDB / ID: 5muz
TitleStructure of a 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.776 Å
AuthorsRosenthal, M. / Gogrefe, N. / Reguera, J. / Vogel, D. / Rauschenberger, B. / Cusack, S. / Gunther, S. / Reindl, S.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research FoundationRE 3712/1-1 Germany
German Research FoundationGU 883/1-1 Germany
German Research FoundationGU 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
Revision 1.2Mar 14, 2018Group: Author supporting evidence / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: L protein
B: L protein


Theoretical massNumber of molelcules
Total (without water)23,4562
Polymers23,4562
Non-polymers00
Water1,69394
1
A: L protein


Theoretical massNumber of molelcules
Total (without water)11,7281
Polymers11,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L protein


Theoretical massNumber of molelcules
Total (without water)11,7281
Polymers11,7281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.830, 42.870, 70.830
Angle α, β, γ (deg.)90.00, 114.44, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1942-

HOH

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Components

#1: Protein L protein


Mass: 11728.112 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP Residues 1794-1894
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAS virus / Production host: Escherichia coli (E. coli) / References: UniProt: J7HBG8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.2 Å3/Da / Density % sol: 44.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris, pH 7.9, 1.3 M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.776→64.48 Å / Num. obs: 19347 / % possible obs: 97 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.02015 / Rrim(I) all: 0.02849 / Net I/σ(I): 7.41
Reflection shellResolution: 1.776→1.84 Å / Redundancy: 2 % / Num. unique obs: 1919 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLM7.1.3data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MUS

5mus


Resolution: 1.776→64.48 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.08
RfactorNum. reflection% reflection
Rfree0.2808 993 5.14 %
Rwork0.2139 --
obs0.217 19334 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.776→64.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1548 0 0 94 1642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081598
X-RAY DIFFRACTIONf_angle_d0.9992167
X-RAY DIFFRACTIONf_dihedral_angle_d18.271961
X-RAY DIFFRACTIONf_chiral_restr0.063240
X-RAY DIFFRACTIONf_plane_restr0.007277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.776-1.86970.38991780.33122590X-RAY DIFFRACTION97
1.8697-1.98680.35131320.29842567X-RAY DIFFRACTION97
1.9868-2.14020.33171320.27212621X-RAY DIFFRACTION96
2.1402-2.35560.30591580.26262583X-RAY DIFFRACTION97
2.3556-2.69650.26841100.25092643X-RAY DIFFRACTION97
2.6965-3.39730.30371440.22752632X-RAY DIFFRACTION97
3.3973-64.52370.24071390.16842705X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 49.7215 Å / Origin y: -18.981 Å / Origin z: 81.4092 Å
111213212223313233
T0.2099 Å2-0.0602 Å20.0158 Å2-0.3666 Å2-0.0221 Å2--0.1967 Å2
L1.5235 °2-1.0469 °20.0499 °2-5.6579 °2-0.5771 °2--0.4572 °2
S-0.0221 Å °-0.1043 Å °0.0547 Å °-0.0453 Å °0.1504 Å °0.0479 Å °-0.0003 Å °0.0474 Å °-0.1118 Å °
Refinement TLS groupSelection details: all

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