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- PDB-5lrp: Mopeia Virus Exonuclease domain complexed with Magnesium -

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Basic information

Entry
Database: PDB / ID: 5lrp
TitleMopeia Virus Exonuclease domain complexed with Magnesium
ComponentsNucleoprotein
KeywordsHYDROLASE / Mopeia virus / Exonuclease Magnesium
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IKBKE activity / RNA-templated viral transcription / negative stranded viral RNA replication / helical viral capsid / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / viral nucleocapsid / host cell cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding / metal ion binding
Similarity search - Function
Nucleocapsid protein, arenaviridae / Nucleocapsid, N-terminal, Arenaviridae / Nucleocapsid, C-terminal, Arenaviridae / Nucleocapsid, C-terminal superfamily / Arenavirus nucleocapsid N-terminal domain / Arenavirus nucleocapsid C-terminal domain
Similarity search - Domain/homology
Biological speciesMopeia virus AN20410
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.941 Å
AuthorsYekwa, E.L. / Khourieh, J. / Canard, B. / Ferron, F.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-BSV8-0019 France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Activity inhibition and crystal polymorphism induced by active-site metal swapping.
Authors: Yekwa, E. / Khourieh, J. / Canard, B. / Papageorgiou, N. / Ferron, F.
History
DepositionAug 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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_author.name
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 17, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.4Jan 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: Nucleoprotein
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3056
Polymers47,1262
Non-polymers1794
Water5,206289
1
A: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6533
Polymers23,5631
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,6533
Polymers23,5631
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.439, 38.182, 137.093
Angle α, β, γ (deg.)90.00, 91.99, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-859-

HOH

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein


Mass: 23563.014 Da / Num. of mol.: 2 / Fragment: exonuclease domain, UNP residues 365-570
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mopeia virus AN20410 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: Q5S581
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.56 Å3/Da / Density % sol: 40.3 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M MES pH 6.5, 25 % (M/W) PEG 8000

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 13, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.941→45.41 Å / Num. obs: 35271 / % possible obs: 99.71 % / Redundancy: 2 % / Net I/σ(I): 14.88
Reflection shellResolution: 1.941→2.01 Å / Redundancy: 2 % / % possible all: 98.28

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSVERSION November 3, 2014data reduction
XDSdata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q7B

3q7b


Resolution: 1.941→45.41 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.72
RfactorNum. reflection% reflection
Rfree0.2447 1712 4.86 %
Rwork0.195 --
obs0.1973 35224 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.941→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 4 289 3595
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093420
X-RAY DIFFRACTIONf_angle_d1.2234602
X-RAY DIFFRACTIONf_dihedral_angle_d13.2791338
X-RAY DIFFRACTIONf_chiral_restr0.049506
X-RAY DIFFRACTIONf_plane_restr0.006605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9411-1.99820.28751580.23312716X-RAY DIFFRACTION98
1.9982-2.06270.35011590.24022745X-RAY DIFFRACTION99
2.0627-2.13640.26251260.22752764X-RAY DIFFRACTION99
2.1364-2.22190.28091320.22492760X-RAY DIFFRACTION99
2.2219-2.32310.26621740.21182732X-RAY DIFFRACTION100
2.3231-2.44550.2571370.20682781X-RAY DIFFRACTION100
2.4455-2.59870.2481400.21672801X-RAY DIFFRACTION100
2.5987-2.79940.30041240.22472819X-RAY DIFFRACTION100
2.7994-3.0810.28071350.21682811X-RAY DIFFRACTION100
3.081-3.52670.2461320.19812840X-RAY DIFFRACTION100
3.5267-4.44270.20381510.1672805X-RAY DIFFRACTION100
4.4427-45.42390.20771440.16512938X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.79870.4942-0.00840.5952-0.34452.19570.13250.0676-0.0213-0.1547-0.0973-0.03890.18490.01450.00090.22260.07850.01220.1167-0.0020.1859.05384.0997187.8651
20.691-0.0281-0.07080.2516-0.01660.0320.19390.65270.0177-0.31290.1691-0.2524-0.00260.31880.02390.25370.07430.05180.4325-0.00550.316780.92069.5394180.5877
30.91470.1778-0.34720.1476-0.12590.35270.23420.60180.3823-0.1252-0.10410.0265-0.004-0.39460.08130.26840.16160.03220.20820.06620.234957.333410.1022180.3136
40.27440.03310.31030.00220.03060.34380.11880.63060.01320.2578-0.118-0.128-0.16480.4997-0.15660.51860.11430.05540.1847-0.03680.443156.585727.5709201.9552
52.5004-0.57541.37911.4201-0.40623.5504-0.0785-0.1208-0.0808-0.07190.07050.0932-0.0628-0.2304-0.00010.17260.0593-0.01680.25050.01470.246445.085621.1117154.8285
60.0365-0.0666-0.12820.21580.34660.59370.4552-0.30330.27960.1349-0.3578-0.07940.5521-0.50770.06810.48110.117101.2276-0.06910.448322.581129.0894164.2417
70.3864-0.27420.09890.36720.36470.575-0.2677-0.21210.26810.11680.13730.0765-0.57880.0772-0.06610.32440.0554-0.02870.34810.00620.27247.627727.9141161.3566
80.1517-0.0826-0.08440.82270.30220.1275-0.169-0.48810.44530.2166-0.04890.337-0.3271-0.16220.00410.78330.0963-0.07890.3465-0.05430.503845.525842.7941141.4432
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 511 )
2X-RAY DIFFRACTION2chain 'A' and (resid 512 through 527)
3X-RAY DIFFRACTION3chain 'A' and (resid 528 through 561)
4X-RAY DIFFRACTION4chain 'A' and (resid 562 through 570)
5X-RAY DIFFRACTION5chain 'B' and (resid 365 through 511 )
6X-RAY DIFFRACTION6chain 'B' and (resid 512 through 527)
7X-RAY DIFFRACTION7chain 'B' and (resid 528 through 561 )
8X-RAY DIFFRACTION8chain 'B' and (resid 562 through 570 )

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