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- PDB-6dwx: Crystal structure of SeMet phased viral OTU domain protease from ... -

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Basic information

Entry
Database: PDB / ID: 6dwx
TitleCrystal structure of SeMet phased viral OTU domain protease from Qalyub virus
ComponentsRNA-dependent RNA polymerase
KeywordsHYDROLASE / PROTEIN BINDING / viral OTU / DUB / VIRAL PROTEIN
Function / homology
Function and homology information


protein deubiquitination / cysteine-type deubiquitinase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription
Similarity search - Function
: / : / OTU-like cysteine protease / OTU domain / OTU domain profile. / 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
RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesQualyub virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.395 Å
AuthorsDzimianski, J.V. / Beldon, B.S. / Daczkowski, C.M. / Goodwin, O.Y. / Pegan, S.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI109008 United States
CitationJournal: PLoS Pathog. / Year: 2019
Title: Probing the impact of nairovirus genomic diversity on viral ovarian tumor domain protease (vOTU) structure and deubiquitinase activity.
Authors: Dzimianski, J.V. / Beldon, B.S. / Daczkowski, C.M. / Goodwin, O.Y. / Scholte, F.E.M. / Bergeron, E. / Pegan, S.D.
History
DepositionJun 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)61,9613
Polymers61,9613
Non-polymers00
Water2,216123
1
A: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,6541
Polymers20,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,6541
Polymers20,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,6541
Polymers20,6541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.587, 110.587, 106.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 20653.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Qualyub virus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A191KWB3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M magnesium acetate, 16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.395→50 Å / Num. obs: 29866 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 0.99 / Net I/σ(I): 80.65
Reflection shellResolution: 2.395→2.44 Å / Mean I/σ(I) obs: 29.9 / Num. unique obs: 2883 / CC1/2: 0.996

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.395→38.301 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1948 2004 6.71 %
Rwork0.1738 --
obs0.1753 29865 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.395→38.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 0 123 3966
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083966
X-RAY DIFFRACTIONf_angle_d0.8255394
X-RAY DIFFRACTIONf_dihedral_angle_d3.5032235
X-RAY DIFFRACTIONf_chiral_restr0.054549
X-RAY DIFFRACTIONf_plane_restr0.005696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3949-2.45480.21691360.18061903X-RAY DIFFRACTION97
2.4548-2.52120.2261380.18291966X-RAY DIFFRACTION100
2.5212-2.59540.24231420.18041961X-RAY DIFFRACTION100
2.5954-2.67910.2331430.19221963X-RAY DIFFRACTION100
2.6791-2.77480.21751430.18881985X-RAY DIFFRACTION100
2.7748-2.88590.20481390.18711988X-RAY DIFFRACTION100
2.8859-3.01720.221410.18091962X-RAY DIFFRACTION100
3.0172-3.17620.21421460.17932002X-RAY DIFFRACTION100
3.1762-3.37510.20571400.18421977X-RAY DIFFRACTION100
3.3751-3.63550.19891440.17451984X-RAY DIFFRACTION100
3.6355-4.0010.16911420.15632004X-RAY DIFFRACTION100
4.001-4.57910.15451470.14882024X-RAY DIFFRACTION100
4.5791-5.76610.18291460.16422036X-RAY DIFFRACTION100
5.7661-38.30630.19171570.19192106X-RAY DIFFRACTION100

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