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- PDB-5ltf: Crystal structure of Lymphocytic choriomeningitis mammarenavirus ... -

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Basic information

Entry
Database: PDB / ID: 5ltf
TitleCrystal structure of Lymphocytic choriomeningitis mammarenavirus endonuclease complexed with catalytic ions
ComponentsRNA-directed RNA polymerase L
KeywordsTRANSFERASE / Endonuclease / LCMV Arenavirus
Function / homology
Function and homology information


RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity ...RNA-templated viral transcription / negative stranded viral RNA replication / cap snatching / virion component / host cell / Hydrolases; Acting on ester bonds / host cell cytoplasm / hydrolase activity / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / nucleotide binding / metal ion binding
Similarity search - Function
Arenavirus RNA polymerase / 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. / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA-directed RNA polymerase L / RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesLymphocytic choriomeningitis mammarenavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsSaez-Ayala, M. / Yekwa, E.L. / Canard, B. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR11-BSV8-0019 France
CitationJournal: IUCrJ / Year: 2018
Title: Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands.
Authors: Saez-Ayala, M. / Yekwa, E.L. / Carcelli, M. / Canard, B. / Alvarez, K. / Ferron, F.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 30, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: RNA-directed RNA polymerase L
A: RNA-directed RNA polymerase L
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4934
Polymers47,4442
Non-polymers492
Water2,846158
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-18 kcal/mol
Surface area21040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.361, 108.361, 54.106
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein RNA-directed RNA polymerase L / Protein L


Mass: 23722.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lymphocytic choriomeningitis mammarenavirus
Gene: L, KUE_IGS320002 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A059U381, UniProt: P14240*PLUS, RNA-directed RNA polymerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: sodium citrate 0,1M pH 6,2, Isopropanol 3,5%, MgCl2 1mM

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.43→48.46 Å / Num. obs: 67793 / % possible obs: 96 % / Redundancy: 2.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04644 / Net I/σ(I): 13.61
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 2.9 % / CC1/2: 0.586 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JSB

3jsb


Resolution: 2.43→48.46 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.97
RfactorNum. reflection% reflection
Rfree0.2336 1932 8.4 %
Rwork0.1837 --
obs0.188 23000 96.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.43→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3080 0 2 158 3240
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093134
X-RAY DIFFRACTIONf_angle_d1.0824235
X-RAY DIFFRACTIONf_dihedral_angle_d17.6651922
X-RAY DIFFRACTIONf_chiral_restr0.056484
X-RAY DIFFRACTIONf_plane_restr0.007550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.49050.35721160.28231287X-RAY DIFFRACTION85
2.4905-2.55790.33131350.26031451X-RAY DIFFRACTION92
2.5579-2.63310.32081320.26551452X-RAY DIFFRACTION93
2.6331-2.71810.33411350.24861491X-RAY DIFFRACTION96
2.7181-2.81530.29131440.23331500X-RAY DIFFRACTION97
2.8153-2.9280.33981350.24761514X-RAY DIFFRACTION98
2.928-3.06120.26911420.23171550X-RAY DIFFRACTION98
3.0612-3.22260.28331390.21611492X-RAY DIFFRACTION97
3.2226-3.42440.28931450.20221565X-RAY DIFFRACTION99
3.4244-3.68870.2631400.20051535X-RAY DIFFRACTION98
3.6887-4.05980.21441440.16371544X-RAY DIFFRACTION98
4.0598-4.64680.18971390.15621556X-RAY DIFFRACTION98
4.6468-5.85290.21061390.15881536X-RAY DIFFRACTION98
5.8529-100.16811470.14621595X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -39.0485 Å / Origin y: -2.5774 Å / Origin z: -3.0292 Å
111213212223313233
T0.4684 Å20.0053 Å2-0.0171 Å2-0.4981 Å20.0626 Å2--0.4676 Å2
L0.1902 °20.0329 °2-0.027 °2-1.036 °2-0.4687 °2--0.59 °2
S0.0446 Å °0.0942 Å °0.0491 Å °-0.0034 Å °-0.0559 Å °-0.0088 Å °-0.005 Å °0.0117 Å °0.0185 Å °
Refinement TLS groupSelection details: all

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