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- PDB-4lmt: Structure of The N-terminal domain of Coronavirus Nucleocapsid Pr... -

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Basic information

Entry
Database: PDB / ID: 4lmt
TitleStructure of The N-terminal domain of Coronavirus Nucleocapsid Protein complexed with NSC663284
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / HCoV-OC43 / Nucleocapsid prtoein / N-termainl domain / RNA binding
Function / homology
Function and homology information


host cell / host cell endoplasmic reticulum-Golgi intermediate compartment / viral nucleocapsid / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, betacoronavirus / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile.
Similarity search - Domain/homology
Chem-CQD / Nucleoprotein / Nucleocapsid protein
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLin, S.Y. / Liu, C.L. / Hou, M.H.
CitationJournal: To be Published
Title: Domain of Coronavirus Nucleocapsid Protein complexed with NSC663284
Authors: Lin, S.Y. / Liu, C.L. / Hou, M.H.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Nucleoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7602
Polymers15,4381
Non-polymers3221
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.911, 81.911, 42.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nucleoprotein


Mass: 15437.901 Da / Num. of mol.: 1 / Fragment: UNP residues 55-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus / Strain: OC43 / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SA23, UniProt: P33469*PLUS
#2: Chemical ChemComp-CQD / 6-chloro-7-{[2-(morpholin-4-yl)ethyl]amino}quinoline-5,8-dione


Mass: 321.759 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H16ClN3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

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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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG1500, 0.25M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.71→30 Å / Num. all: 17432 / Num. obs: 17432 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.13 Å2
Reflection shellResolution: 1.71→1.77 Å / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J3K

4j3k


Resolution: 1.71→22.732 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7818 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 28.56 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 1710 9.98 %Random
Rwork0.2359 ---
obs0.2402 17133 92.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.92 Å2 / Biso mean: 20.3821 Å2 / Biso min: 2.75 Å2
Refinement stepCycle: LAST / Resolution: 1.71→22.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1079 0 22 99 1200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081143
X-RAY DIFFRACTIONf_angle_d1.3731563
X-RAY DIFFRACTIONf_chiral_restr0.091154
X-RAY DIFFRACTIONf_plane_restr0.006205
X-RAY DIFFRACTIONf_dihedral_angle_d18.076411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7097-1.760.35091240.25521082120642
1.76-1.81670.28871420.25751281142349
1.8167-1.88160.30911520.26761348150051
1.8816-1.95690.33521430.31191327147051
1.9569-2.0460.31681560.25921347150351
2.046-2.15370.32571480.25061327147551
2.1537-2.28860.31891230.27971087121042
2.2886-2.46510.30411460.25281335148151
2.4651-2.71280.31341490.2561355150451
2.7128-3.10450.26981510.23051346149752
3.1045-3.90810.23431320.20371208134046
3.9081-22.73440.20891440.18531380152453

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