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- PDB-6wc1: Peptide-bound SARS-CoV-2 Nsp9 RNA-replicase -

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Basic information

Entry
Database: PDB / ID: 6wc1
TitlePeptide-bound SARS-CoV-2 Nsp9 RNA-replicase
ComponentsSARS-coV-2 Non-structural protein 9
KeywordsVIRAL PROTEIN / COVID-19 / SARS-CoV-2 / Nsp9 / RNA replicase
Function / homologyCoronavirus replicase NSP9
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLittler, D.R. / Gully, B.S. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: To Be Published
Title: Identification of a putative peptide-binding site at the dimer interface of the SARS-CoV-2 Nsp9 RNA-replicase.
Authors: Littler, D.R. / Gully, B.S. / Colson, R.N. / Riboldi-Tunnicliffe, A. / Rossjohn, J.
History
DepositionMar 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: SARS-coV-2 Non-structural protein 9
B: SARS-coV-2 Non-structural protein 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3013
Polymers25,2052
Non-polymers961
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-33 kcal/mol
Surface area12310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.670, 88.670, 134.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein SARS-coV-2 Non-structural protein 9


Mass: 12602.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.25 Å3/Da / Density % sol: 62.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 2-2.4M AmSO4, 0.1M phosphate citrate pH 4 / PH range: 4-4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.541 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 1, 2020
RadiationMonochromator: Capillary optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.4→76.8 Å / Num. obs: 12038 / % possible obs: 94.8 % / Redundancy: 16.2 % / Biso Wilson estimate: 52.4 Å2 / Rpim(I) all: 0.018 / Net I/σ(I): 23.4
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1307 / Rpim(I) all: 0.291 / % possible all: 73.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Qz8

1qz8


Resolution: 2.4→76.8 Å / SU ML: 0.3205 / Cross valid method: FREE R-VALUE / Phase error: 32.1592
RfactorNum. reflection% reflection
Rfree0.278 603 5.04 %
Rwork0.232 --
obs0.2344 11971 93.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→76.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1717 0 0 8 1725
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571748
X-RAY DIFFRACTIONf_angle_d0.94352373
X-RAY DIFFRACTIONf_chiral_restr0.3161275
X-RAY DIFFRACTIONf_plane_restr0.0047302
X-RAY DIFFRACTIONf_dihedral_angle_d24.6066643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.35591240.31642356X-RAY DIFFRACTION80.03
2.64-3.020.33791400.28592906X-RAY DIFFRACTION97.97
3.02-3.810.29591670.25292951X-RAY DIFFRACTION98.11
3.81-38.610.24861720.20123155X-RAY DIFFRACTION98.69
Refinement TLS params.Method: refined / Origin x: 41.4524517318 Å / Origin y: -12.557527235 Å / Origin z: 16.4318149353 Å
111213212223313233
T0.453544412626 Å20.0253586450189 Å20.0915278247565 Å2-0.240355952502 Å20.0318432027579 Å2--0.340311307912 Å2
L4.44199136211 °20.0560362785456 °21.33371801237 °2-1.25488716167 °20.0150618520974 °2--2.32738992852 °2
S-0.0188102029667 Å °0.170963235238 Å °0.278965775966 Å °-0.044503150179 Å °0.0260140169772 Å °0.0718722617812 Å °0.00437993030432 Å °0.0110240594238 Å °-0.00272634637296 Å °
Refinement TLS groupSelection details: all

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