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- PDB-2ckw: The 2.3 A resolution structure of the Sapporo virus RNA dependant... -

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Basic information

Entry
Database: PDB / ID: 2ckw
TitleThe 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.
ComponentsRNA-DIRECTED RNA POLYMERASERNA-dependent RNA polymerase
KeywordsHYDROLASE / NUCLEOTIDE-BINDING / NUCLEOTIDYLTRANSFERASE / COVALENT PROTEIN-RNA LINKAGE / POLYMERASE / RNA ELONGATION / TRANSFERASE ACTIVITY / MUTANT / CAPSID PROTEIN / RNA REPLICATION / STRUCTURAL PROTEIN / PROTEASE / HELICASE / TRANSFERASE / RNA-DIRECTED RNA POLYMERASE / POLYPROTEIN / ATP-BINDING / THIOL PROTEASE
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / DNA replication / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / host cell cytoplasm / RNA helicase activity / DNA replication / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding
Similarity search - Function
: / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A ...: / Viral genome-linked protein / Caliciviridae (CV) 3C-like protein profile. / Peptidase C24, Calicivirus polyprotein Orf1 / 2C endopeptidase (C24) cysteine protease family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Calicivirus coat protein / Calicivirus coat protein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Helix non-globular / Viral coat protein subunit / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesSAPPORO VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFullerton, S.W.B. / Tucker, P.A. / Rohayem, J. / Coutard, B. / Gebhardt, J. / Gorbalenya, A. / Canard, B.
CitationJournal: J.Virol. / Year: 2007
Title: Structural and Functional Characterization of Sapovirus RNA-Dependent RNA Polymerase.
Authors: Fullerton, S.W.B. / Blaschke, M. / Coutard, B. / Gebhardt, J. / Gorbalenya, A. / Canard, B. / Tucker, P.A. / Rohayem, J.
History
DepositionApr 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 16, 2019Group: Data collection / Other / Category: pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.5Dec 13, 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-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)56,4861
Polymers56,4861
Non-polymers00
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.434, 93.881, 94.771
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RNA-dependent RNA polymerase / SAPOVIRUS RNA-DEPENDANT RNA-POLYMERASE


Mass: 56485.711 Da / Num. of mol.: 1 / Fragment: RNA POLYMERASE, RESIDUES 1135-1649
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SAPPORO VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q69014, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.29 Å3/Da / Density % sol: 45.77 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.961
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.961 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 27029 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.2
Reflection shellResolution: 2.32→2.46 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.4 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KHV

1khv


Resolution: 2.3→66.67 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.905 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1209 5.1 %RANDOM
Rwork0.171 ---
obs0.174 22378 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 0 271 4037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0223899
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4611.955323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2795490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.45423.976166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.30415606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4391521
X-RAY DIFFRACTIONr_chiral_restr0.2080.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022991
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2840.21920
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22663
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.581.52518
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.45523982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.93931589
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.9874.51341
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 81 -
Rwork0.176 1659 -
obs--100 %

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