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- PDB-5cx6: Crystal structure of Thosea asigna virus RNA-dependent RNA polyme... -

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Basic information

Entry
Database: PDB / ID: 5cx6
TitleCrystal structure of Thosea asigna virus RNA-dependent RNA polymerase (RdRP) complexed with CDP
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE / RdRP / complex / CDP
Function / homologyRNA-dependent RNA polymerase activity / DNA/RNA polymerase superfamily / ATP binding / CYTIDINE-5'-DIPHOSPHATE / RNA-dependent RNA polymerase
Function and homology information
Biological speciesThosea asigna virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFerrero, D.S. / Buxaderas, M. / Rodriguez, J.F. / Verdaguer, N.
Funding support Spain, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBIO2011-24333 Spain
Spanish Ministry of Economy and CompetitivenessAGL2011-24758 Spain
European Union SILVER Large Scale Collaborative Project260644
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
DepositionJul 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_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-dependent RNA polymerase
B: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,81436
Polymers159,0812
Non-polymers3,73334
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-230 kcal/mol
Surface area54540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.700, 149.600, 100.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA-dependent RNA polymerase /


Mass: 79540.461 Da / Num. of mol.: 2 / Fragment: UNP residues 1-674
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thosea asigna virus / Gene: RdRp / Plasmid: pFastBac1-HM / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6A562

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Non-polymers , 5 types, 637 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, Lithium sulfate

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→66.85 Å / Num. obs: 115494 / % possible obs: 98.31 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 5.64
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 3 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.8 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XHI

4xhi


Resolution: 2.1→66.85 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 5790 5.02 %Random selection
Rwork0.1836 ---
obs0.1861 115444 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→66.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10512 0 221 603 11336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710931
X-RAY DIFFRACTIONf_angle_d1.06214786
X-RAY DIFFRACTIONf_dihedral_angle_d14.8414060
X-RAY DIFFRACTIONf_chiral_restr0.0411600
X-RAY DIFFRACTIONf_plane_restr0.0051884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.28171970.23983584X-RAY DIFFRACTION98
2.1239-2.14890.29472020.25093586X-RAY DIFFRACTION98
2.1489-2.17510.30951900.24633614X-RAY DIFFRACTION98
2.1751-2.20260.28171720.23823529X-RAY DIFFRACTION96
2.2026-2.23160.27151820.23063528X-RAY DIFFRACTION95
2.2316-2.26220.2831970.22623599X-RAY DIFFRACTION99
2.2622-2.29450.28181980.21613643X-RAY DIFFRACTION99
2.2945-2.32870.26851800.20693685X-RAY DIFFRACTION100
2.3287-2.36510.25251960.20553666X-RAY DIFFRACTION99
2.3651-2.40390.25242050.20473632X-RAY DIFFRACTION99
2.4039-2.44530.26851950.19923668X-RAY DIFFRACTION99
2.4453-2.48980.23611880.19773670X-RAY DIFFRACTION99
2.4898-2.53770.26692000.19673638X-RAY DIFFRACTION99
2.5377-2.58950.23421820.19353603X-RAY DIFFRACTION98
2.5895-2.64580.25062210.19823596X-RAY DIFFRACTION97
2.6458-2.70740.28171910.20293498X-RAY DIFFRACTION95
2.7074-2.77510.24412050.20523654X-RAY DIFFRACTION99
2.7751-2.85010.25722010.193680X-RAY DIFFRACTION100
2.8501-2.9340.24921870.1893709X-RAY DIFFRACTION100
2.934-3.02870.25581800.19223695X-RAY DIFFRACTION99
3.0287-3.13690.24861840.19683687X-RAY DIFFRACTION99
3.1369-3.26250.24261830.19923729X-RAY DIFFRACTION99
3.2625-3.4110.22751770.18683655X-RAY DIFFRACTION98
3.411-3.59080.21082040.16893537X-RAY DIFFRACTION96
3.5908-3.81580.18821990.15423735X-RAY DIFFRACTION100
3.8158-4.11030.20751970.1543736X-RAY DIFFRACTION100
4.1103-4.52390.18482010.14223726X-RAY DIFFRACTION99
4.5239-5.17830.19221950.1413649X-RAY DIFFRACTION96
5.1783-6.52320.20121960.16943786X-RAY DIFFRACTION99
6.5232-66.88390.21781850.17923937X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 24.6923 Å / Origin y: 31.1448 Å / Origin z: 23.2677 Å
111213212223313233
T0.1572 Å2-0.0327 Å20.0074 Å2-0.1602 Å2-0.0071 Å2--0.2047 Å2
L0.0763 °2-0.0827 °20.0857 °2-0.0827 °2-0.1102 °2--0.595 °2
S0.0129 Å °0.0021 Å °-0.0042 Å °0.0236 Å °0.0124 Å °0.0099 Å °0.0186 Å °0.0037 Å °-0.0307 Å °
Refinement TLS groupSelection details: all

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