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- PDB-7y5m: The OTU domain of Tacheng Tick Virus 1 -

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Basic information

Entry
Database: PDB / ID: 7y5m
TitleThe OTU domain of Tacheng Tick Virus 1
ComponentsRNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / membrane
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.
Similarity search - Domain/homology
RNA-directed RNA polymerase L
Similarity search - Component
Biological speciesTacheng Tick Virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, Z. / Wang, W.J. / Xiao, Y.S. / Sun, L.T.
Funding support7items
OrganizationGrant numberCountry
Other governmentJCYJ20190807155011406
Other governmentKQTD20180411143323605
Other governmentGXWD20201231165807008
Other government20200825113322001
Other governmentJSGG20200225152008136
Other government2021B1515020047
Other government31971147
CitationJournal: To Be Published
Title: The OTU domain of Tacheng Tick Virus 1
Authors: Li, Z. / Wang, W.J. / Xiao, Y.S. / Sun, L.T.
History
DepositionJun 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Source and taxonomy / Category: chem_comp_atom / chem_comp_bond / entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)19,2301
Polymers19,2301
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8030 Å2
Unit cell
Length a, b, c (Å)47.747, 58.110, 59.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase / Replicase / Transcriptase


Mass: 19229.670 Da / Num. of mol.: 1 / Fragment: OTU domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tacheng Tick Virus 1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B5KXW6, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: PEG 4000,Lithium sulfate monohydrate,MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 27019 / % possible obs: 99.5 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.54 Å2 / CC1/2: 0.976 / Net I/σ(I): 15.3
Reflection shellResolution: 1.5→1.55 Å / Num. unique obs: 2598 / CC1/2: 0.813

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PHU

3phu


Resolution: 1.5→18.75 Å / SU ML: 0.1667 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9014
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 1330 4.99 %
Rwork0.1977 25315 -
obs0.1993 26645 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.43 Å2
Refinement stepCycle: LAST / Resolution: 1.5→18.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1237 0 0 136 1373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571270
X-RAY DIFFRACTIONf_angle_d0.89541730
X-RAY DIFFRACTIONf_chiral_restr0.088192
X-RAY DIFFRACTIONf_plane_restr0.0073222
X-RAY DIFFRACTIONf_dihedral_angle_d6.0088166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.28051300.2252529X-RAY DIFFRACTION90.53
1.56-1.630.23831540.21412767X-RAY DIFFRACTION98.05
1.63-1.720.24991430.21092769X-RAY DIFFRACTION98.48
1.72-1.820.22861570.20932783X-RAY DIFFRACTION99.12
1.82-1.970.24021350.19262848X-RAY DIFFRACTION99.5
1.97-2.160.21651330.19122855X-RAY DIFFRACTION99.77
2.16-2.470.2221660.19662849X-RAY DIFFRACTION99.83
2.47-3.120.24331560.20582895X-RAY DIFFRACTION99.97
3.12-18.750.21881560.18713020X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: 1.24717073409 Å / Origin y: 12.8360933563 Å / Origin z: -15.7325286471 Å
111213212223313233
T0.0967446039851 Å2-0.00674586569498 Å2-0.00686224479664 Å2-0.0796758486331 Å2-0.0112718192053 Å2--0.0745852678195 Å2
L1.95752428963 °2-0.232468188867 °2-0.0955345200466 °2-1.07196926741 °2-0.0640592443713 °2--0.9169876386 °2
S0.0388086394448 Å °-0.0646230837291 Å °-0.0103469219921 Å °0.0346926318353 Å °-0.00876414405034 Å °-0.0132570850206 Å °-0.0193013678648 Å °0.021683173754 Å °-0.0264669192785 Å °
Refinement TLS groupSelection details: all

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