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- PDB-6q99: Ande virus L protein N-terminus mutant K124A -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6q99
TitleAnde virus L protein N-terminus mutant K124A
ComponentsRNA polymerase
KeywordsVIRAL PROTEIN / Andes virus / nuclease / L protein / cap-snatching
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription
Similarity search - Function
RNA-directed RNA polymerase, hantavirus / RNA-directed RNA polymerase, hantavirus, N-terminal / RNA dependent RNA polymerase / RNA-dependent RNA polymerase, bunyaviral / Bunyavirus RNA dependent RNA polymerase / RNA-directed RNA polymerase, negative-strand RNA virus / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile.
Similarity search - Domain/homology
MANGANESE (III) ION / Replicase
Similarity search - Component
Biological speciesAndes orthohantavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.951 Å
AuthorsFernandez-Garcia, Y. / Holm, T. / Kirchmair, J. / Wurr, S. / Gunther, S. / Reindl, S.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchIB-045 Germany
German Research FoundationRE 3712/1-1 Germany
CitationJournal: To Be Published
Title: Specific inhibition of a diverse set of segmented negative strand viruses by a single molecule
Authors: Fernandez-Garcia, Y. / Kirchmair, J. / Holm, T. / Wurr, S. / Gunther, S. / Reindl, S.
History
DepositionDec 17, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionJan 15, 2020ID: 5HSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2994
Polymers23,0981
Non-polymers2023
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SAXS data already published
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-12 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.341, 82.341, 79.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein RNA polymerase


Mass: 23097.523 Da / Num. of mol.: 1 / Mutation: K124A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Andes orthohantavirus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9E005
#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 400mM (NH4)2SO4, 27% PEG3350, 100mM NaAc pH5.5, 10mM MnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.951→79.6 Å / Num. obs: 6154 / % possible obs: 99.95 % / Redundancy: 2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.05054 / Rrim(I) all: 0.071 / Net I/σ(I): 9.2
Reflection shellResolution: 2.951→3.056 Å / Redundancy: 2 % / Rmerge(I) obs: 0.1209 / Mean I/σ(I) obs: 4.77 / Num. unique obs: 591 / CC1/2: 0.565 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HSB

5hsb
PDB Unreleased entry


Resolution: 2.951→79.599 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 30.92
RfactorNum. reflection% reflection
Rfree0.3133 611 9.93 %
Rwork0.2384 --
obs0.246 6153 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.951→79.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 8 5 1625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131647
X-RAY DIFFRACTIONf_angle_d1.3122225
X-RAY DIFFRACTIONf_dihedral_angle_d17.912635
X-RAY DIFFRACTIONf_chiral_restr0.06249
X-RAY DIFFRACTIONf_plane_restr0.007289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9511-3.24810.37681450.28851336X-RAY DIFFRACTION100
3.2481-3.71810.36441500.26671362X-RAY DIFFRACTION100
3.7181-4.68430.25691520.20851373X-RAY DIFFRACTION100
4.6843-79.62780.29661640.21831471X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 176.8885 Å / Origin y: 149.4285 Å / Origin z: 95.4819 Å
111213212223313233
T0.1671 Å2-0.0819 Å20.0436 Å2-0.1977 Å20.001 Å2--0.3516 Å2
L0.9728 °20.0188 °20.4539 °2-1.3196 °2-0.3636 °2--0.9511 °2
S0.0627 Å °-0.3926 Å °0.1764 Å °-0.0227 Å °-0.007 Å °0.2317 Å °-0.0222 Å °-0.1824 Å °-0.0415 Å °
Refinement TLS groupSelection details: all

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