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- PDB-6dx2: Crystal structure of the viral OTU domain protease from Dera Ghaz... -

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Basic information

Entry
Database: PDB / ID: 6dx2
TitleCrystal structure of the viral OTU domain protease from Dera Ghazi Khan virus
ComponentsRNA-dependent RNA polymerase
KeywordsHYDROLASE / PROTEIN BINDING / viral OTU / DUB / Viral Protein
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
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. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesDera Ghazi Khan orthonairovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.614 Å
AuthorsBeldon, B.S. / Dzimianski, J.V. / 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 11, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,0252
Polymers40,0252
Non-polymers00
Water3,297183
1
A: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,0121
Polymers20,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-dependent RNA polymerase


Theoretical massNumber of molelcules
Total (without water)20,0121
Polymers20,0121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.417, 68.417, 69.769
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-dependent RNA polymerase /


Mass: 20012.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dera Ghazi Khan orthonairovirus / Production host: Escherichia coli (E. coli) / References: UniProt: A0A191KW82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M citric acid pH 3.5, 13% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.614→50 Å / Num. obs: 40786 / % possible obs: 99 % / Redundancy: 4.9 % / CC1/2: 0.99 / Net I/σ(I): 24.8
Reflection shellResolution: 1.614→1.65 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3932 / CC1/2: 0.568

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DX1

6dx1


Resolution: 1.614→28.021 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.45
RfactorNum. reflection% reflection
Rfree0.2127 2008 4.92 %
Rwork0.1794 --
obs0.1809 40772 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.614→28.021 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 0 183 2675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142554
X-RAY DIFFRACTIONf_angle_d1.2593472
X-RAY DIFFRACTIONf_dihedral_angle_d3.5981484
X-RAY DIFFRACTIONf_chiral_restr0.073374
X-RAY DIFFRACTIONf_plane_restr0.01446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6144-1.65480.32171240.31212642X-RAY DIFFRACTION94
1.6548-1.69950.34531430.28592798X-RAY DIFFRACTION100
1.6995-1.74950.29091310.24882818X-RAY DIFFRACTION100
1.7495-1.8060.23891840.2292752X-RAY DIFFRACTION100
1.806-1.87050.23421310.20752791X-RAY DIFFRACTION100
1.8705-1.94540.25361460.19772783X-RAY DIFFRACTION100
1.9454-2.03390.24721480.20512798X-RAY DIFFRACTION100
2.0339-2.14110.20861830.19212773X-RAY DIFFRACTION100
2.1411-2.27520.21351740.17562787X-RAY DIFFRACTION100
2.2752-2.45070.22661450.17972792X-RAY DIFFRACTION100
2.4507-2.69720.23951760.18082779X-RAY DIFFRACTION100
2.6972-3.08710.2428990.17342857X-RAY DIFFRACTION100
3.0871-3.88770.17941450.16342833X-RAY DIFFRACTION100
3.8877-28.02510.1843790.17082561X-RAY DIFFRACTION87
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)
10.1769-0.110.32340.5971-0.34920.6296-0.3776-0.5764-0.39410.36560.14340.20460.7886-0.1656-0.00090.4979-0.044-0.01050.4192-0.0220.5394-24.5419-17.8233-5.747
20.7920.08770.63441.016-1.0421.3361-0.0057-0.12310.1027-0.25650.11580.2152-0.0728-0.0533-0.00040.370.00520.0080.3472-0.01590.4044-26.1541-3.6695-6.3187
31.70981.0509-0.91182.4003-1.0823.53270.0156-0.28080.09970.0248-0.203-0.3553-0.18810.5557-0.00010.303-0.0007-0.0350.37780.03080.3273-7.9199-2.50760.6138
42.77791.0155-0.76572.06211.51522.09680.06960.19380.2693-0.3666-0.04550.243-0.2937-0.16020.00050.34540.0297-0.00020.30710.03630.3473-23.5004-5.6505-4.798
50.60620.0104-0.08070.19780.44110.87510.16190.36640.4369-0.1602-0.3643-0.7544-0.10890.7968-00.4487-0.04130.00670.5459-0.02440.5612-16.3952-9.667220.058
61.0840.3875-0.80411.47921.20971.41990.0879-0.34880.236-0.0232-0.02410.0389-0.0673-0.04780.00020.33650.0106-0.00560.39250.00450.4026-30.5451-8.074620.8246
72.13820.8428-0.95361.343-0.77633.6861-0.17480.0233-0.3929-0.29330.05040.17990.5933-0.13450.00030.36560.00010.01820.3143-0.02180.3321-31.7119-26.286213.7166
82.32370.77791.33772.8203-0.88052.1024-0.0287-0.37930.21570.25780.05280.2821-0.2128-0.25520.00110.30420.02860.02810.346-0.00510.3264-28.6023-10.670619.1563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 18 )
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 112 )
4X-RAY DIFFRACTION4chain 'A' and (resid 113 through 158 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 18 )
6X-RAY DIFFRACTION6chain 'B' and (resid 19 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 112 )
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 158 )

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