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- PDB-2wk4: Dimeric structure of D347G D348G mutant of the sapporovirus RNA d... -

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Basic information

Entry
Database: PDB / ID: 2wk4
TitleDimeric structure of D347G D348G mutant of the sapporovirus RNA dependent RNA polymerase
ComponentsPROTEASE-POLYMERASE P70
KeywordsHYDROLASE / COVALENT PROTEIN-RNA LINKAGE / NUCLEOTIDYLTRANSFERASE / RNA REPLICATION / PHOSPHORYLATION / RNA ELONGATION / THIOL PROTEASE / CAPSID PROTEIN / ATP-BINDING / HELICASE / PROTEASE
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...calicivirin / ribonucleoside triphosphate phosphatase activity / viral capsid / nucleoside-triphosphate phosphatase / DNA replication / host cell cytoplasm / RNA helicase activity / 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 / Helix non-globular / Picornavirus/Calicivirus coat protein / Special / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / 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: 2.98 Å
AuthorsFullerton, S.W.B. / Robel, I. / Schuldt, L. / Gebhardt, J. / Tucker, P.A. / Rohayem, J.
CitationJournal: To be Published
Title: Dimeric Structure of D347G D348G Mutant of the Sapporovirus Sapporovirus RNA Dependent RNA Polymerase
Authors: Fullerton, S.W.B. / Robel, I. / Schuldt, L. / Gebhardt, J. / Tucker, P.A. / Rohayem, J.
History
DepositionJun 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: 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 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEASE-POLYMERASE P70
B: PROTEASE-POLYMERASE P70
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,0165
Polymers112,7392
Non-polymers2763
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-17.8 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.613, 132.613, 150.582
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 6 / Auth seq-ID: 12 - 502 / Label seq-ID: 12 - 502

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper: (Code: given
Matrix: (-0.9097, -0.3897, 0.1432), (-0.3976, 0.7182, -0.5711), (0.1197, -0.5765, -0.8083)
Vector: 61.2, 16.57, 7.449)

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Components

#1: Protein PROTEASE-POLYMERASE P70 / RNA DEPENDENT RNA POLYMERASE / PRO-POL


Mass: 56369.633 Da / Num. of mol.: 2 / Fragment: RESIDUES 1135-1649 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SAPPORO VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q69014, calicivirin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 1481 TO GLY ENGINEERED RESIDUE IN CHAIN A, ASP 1482 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, ASP 1481 TO GLY ENGINEERED RESIDUE IN CHAIN A, ASP 1482 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 1481 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 1482 TO GLY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.49 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 29506 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 61.1 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 10.8
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / % possible all: 72.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CKW

2ckw


Resolution: 2.98→26.01 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.837 / SU B: 18.818 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.484 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29208 1407 5 %RANDOM
Rwork0.19836 ---
obs0.20309 26572 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.478 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.98→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7690 0 18 209 7917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.95310788
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3455999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.60523.951329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5231542
X-RAY DIFFRACTIONr_chiral_restr0.110.21213
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216043
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.54999
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.09328094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.47832905
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5954.52694
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 3766 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.555
2Bloose positional0.555
1Aloose thermal7.7510
2Bloose thermal7.7510
LS refinement shellResolution: 2.98→3.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.525 81 -
Rwork0.352 1920 -
obs--98.96 %

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