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- PDB-2ge7: Structure of the C-terminal dimerization domain of infectious bro... -

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Basic information

Entry
Database: PDB / ID: 2ge7
TitleStructure of the C-terminal dimerization domain of infectious bronchitis virus nucleocapsid protein
ComponentsNucleocapsid proteinVirus
KeywordsVIRUS/VIRAL PROTEIN/RNA BINDING PROTEIN / Nucleocapsid protein / N protein / Coronavirus / IBV N protein / Dimerization domain / VIRUS-VIRAL PROTEIN-RNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding / identical protein binding
Similarity search - Function
Nucleocapsid protein, gammacoronavirus / Nucleocapsid (N) protein, C-terminal domain, coronavirus / Nucleocapsid (N) protein, N-terminal domain, coronavirus / Coronavirus nucleocapsid (CoV N) protein N-terminal (NTD) domain profile. / Coronavirus nucleocapsid (CoV N) protein C-terminal (CTD) domain profile. / Nucleocapsid protein, coronavirus / Nucleocapsid protein, C-terminal / Nucleocapsid protein, N-terminal / Coronavirus nucleocapsid
Similarity search - Domain/homology
Biological speciesInfectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V.
CitationJournal: J.Virol. / Year: 2006
Title: X-ray structures of the N- and C-terminal domains of a coronavirus nucleocapsid protein: implications for nucleocapsid formation.
Authors: Jayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collisson, E.W. / Lescar, J. / Prasad, B.V.
History
DepositionMar 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Nucleocapsid protein
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)24,2162
Polymers24,2162
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-35 kcal/mol
Surface area10560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.658, 65.707, 91.008
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsDimer in solution and in the assymetric unit

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Components

#1: Protein Nucleocapsid protein / Virus / N structural protein / NC


Mass: 12107.784 Da / Num. of mol.: 2 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bronchitis virus / Genus: Coronavirus / Strain: Gray / Gene: N / Plasmid: pET 41 Ek-LIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P32923
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG 4000, 28.75% to 29.5 %, pH 4.8 Citrate, 0.1 M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 178 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 , 0.9795
DetectorType: SBC-2 / Detector: CCD / Date: Jun 24, 2004
Details: Rosenbaum-Rock monochromator #1 high-resolution double-crystal sagittal focusing, Rosenbaum-Rock monochromator #2 double crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.97951
ReflectionResolution: 1.984→53.452 Å / Num. obs: 15780 / % possible obs: 96 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Limit h max: 18 / Limit h min: 0 / Limit k max: 33 / Limit k min: 0 / Limit l max: 45 / Limit l min: 0 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 28.8
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 0.73 / Rsym value: 0.282 / % possible all: 95

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
CCP4(SCALA)data scaling
SnBphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→53.45 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.922 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.193 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.254 768 5.1 %RANDOM
Rwork0.19 ---
all0.193 28085 --
obs0.193 15127 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.492 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--0.83 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2→53.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 0 92 1778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0221724
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9782325
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4685213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49823.82781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97515301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281514
X-RAY DIFFRACTIONr_chiral_restr0.1870.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021330
X-RAY DIFFRACTIONr_nbd_refined0.2240.2710
X-RAY DIFFRACTIONr_nbtor_refined0.320.21164
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3680.28
X-RAY DIFFRACTIONr_mcbond_it1.3461.51100
X-RAY DIFFRACTIONr_mcangle_it2.15721738
X-RAY DIFFRACTIONr_scbond_it4.0183697
X-RAY DIFFRACTIONr_scangle_it5.954.5587
LS refinement shellResolution: 2.005→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 58 -
Rwork0.209 922 -
obs-980 89.33 %

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