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- PDB-4xhi: Crystal structure of native Thosea asigna virus RNA-dependent RNA... -

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Basic information

Entry
Database: PDB / ID: 4xhi
TitleCrystal structure of native Thosea asigna virus RNA-dependent RNA polymerase (RdRP) at 2.15 Angstrom resolution
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSCRIPTION / Polymerase / virus / RdRP
Function / homology: / : / Permutotetravirus RNA-dependent RNA polymerase palm domain / Permutotetravirus RNA-dependent RNA polymerase thumb domain / RNA-directed RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / metal ion binding / RNA-dependent RNA polymerase
Function and homology information
Biological speciesThosea asigna virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsFerrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2011-24333 Spain
CitationJournal: Plos Pathog. / Year: 2015
Title: The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases.
Authors: Ferrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 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: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,34326
Polymers159,0812
Non-polymers2,26224
Water13,025723
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10790 Å2
ΔGint-206 kcal/mol
Surface area55650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.875, 150.825, 100.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein RNA-dependent RNA polymerase


Mass: 79540.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6A562
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 8K, 750 mM lithium(III) sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→39 Å / Num. obs: 109020 / % possible obs: 97.5 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 9
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 4.1 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHA

4xha


Resolution: 2.15→39.606 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.4 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 4979 5 %
Rwork0.1753 --
obs0.1773 99552 88.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→39.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10504 0 131 723 11358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210876
X-RAY DIFFRACTIONf_angle_d0.64114723
X-RAY DIFFRACTIONf_dihedral_angle_d12.8844044
X-RAY DIFFRACTIONf_chiral_restr0.0251595
X-RAY DIFFRACTIONf_plane_restr0.0031887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1499-2.17430.23122050.19643297X-RAY DIFFRACTION95
2.1743-2.19990.26691660.20323321X-RAY DIFFRACTION95
2.1999-2.22670.27611760.19973351X-RAY DIFFRACTION95
2.2267-2.25490.2678360.19831031X-RAY DIFFRACTION94
2.2549-2.28460.21461270.19782185X-RAY DIFFRACTION93
2.2846-2.31590.24541770.19883270X-RAY DIFFRACTION95
2.3159-2.3490.2541770.19123336X-RAY DIFFRACTION94
2.349-2.3840.23871640.18763327X-RAY DIFFRACTION94
2.384-2.42130.22661760.1913302X-RAY DIFFRACTION94
2.4213-2.4610.24771800.19193320X-RAY DIFFRACTION94
2.461-2.50340.23341760.19173324X-RAY DIFFRACTION94
2.5034-2.54890.23181870.20023492X-RAY DIFFRACTION100
2.5489-2.59790.27861780.19853540X-RAY DIFFRACTION100
2.5979-2.65090.23391910.19863423X-RAY DIFFRACTION100
2.6509-2.70860.2734620.21021129X-RAY DIFFRACTION99
2.7086-2.77160.24931800.20723506X-RAY DIFFRACTION100
2.7716-2.84080.25991800.20383491X-RAY DIFFRACTION100
2.8408-2.91760.23551690.19953561X-RAY DIFFRACTION100
2.9176-3.00350.24432070.19913523X-RAY DIFFRACTION100
3.0035-3.10040.25591770.19683525X-RAY DIFFRACTION100
3.1004-3.21110.2631810.19543536X-RAY DIFFRACTION100
3.2111-3.33960.24342030.18733493X-RAY DIFFRACTION100
3.3396-3.49150.19871230.16682443X-RAY DIFFRACTION68
3.4915-3.67550.2151520.15512815X-RAY DIFFRACTION99
3.6755-3.90560.1911070.14862349X-RAY DIFFRACTION96
3.9056-4.20680.15361540.1363142X-RAY DIFFRACTION100
4.2068-4.62960.15861960.12573552X-RAY DIFFRACTION100
4.6296-5.29820.15841740.13513622X-RAY DIFFRACTION100
5.2982-6.670.17382070.16993616X-RAY DIFFRACTION99
6.67-39.61280.1741910.16213751X-RAY DIFFRACTION98
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)
10.2677-0.0555-0.09650.23820.02820.56680.0194-0.0093-0.00920.032-0.00420.0039-0.0111-0.0432-0.01240.0703-0.0099-0.00310.09770.01320.105113.2186-29.52090.8141
20.1934-0.0337-0.12180.1420.08010.86260.00020.0052-0.00180.03320.0132-0.01010.12630.0291-0.01210.12570.0078-0.01260.0939-0.01010.137236.9713-58.265846.3982
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq -10:9999)
2X-RAY DIFFRACTION2(chain B and resseq -10:9999)

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