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- PDB-2gec: Structure of the N-terminal domain of avian infectious bronchitis... -

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Basic information

Entry
Database: PDB / ID: 2gec
TitleStructure of the N-terminal domain of avian infectious bronchitis virus nucleocapsid protein (strain Gray) in a novel dimeric arrangement
ComponentsNucleocapsid protein
KeywordsVIRAL PROTEIN / Nucleocapsid protein / N protein / Coronavirus / IBV N protein / VIRAL
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 / MOLECULAR REPLACEMENT / Resolution: 1.3 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 19, 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 1.3Aug 30, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleocapsid protein
B: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)31,2212
Polymers31,2212
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.055, 46.210, 74.176
Angle α, β, γ (deg.)90.00, 121.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLYSLYSAA25 - 504 - 29
21PROPROLYSLYSBB25 - 504 - 29
32PHEPHEARGARGAA51 - 7630 - 55
42PHEPHEARGARGBB51 - 7630 - 55
53PHEPHEVALVALAA77 - 8756 - 66
63PHEPHEVALVALBB77 - 8756 - 66
74PROPROASPASPAA88 - 15067 - 129
84PROPROASPASPBB88 - 15067 - 129
DetailsN-terminal domain Possibly dimer in solution. Dimer in the assymetric unit

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Components

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


Mass: 15610.264 Da / Num. of mol.: 2 / Fragment: N-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


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 25 % PEG 4000,100 mM MES Sodium Salt, pH 6.2, 200 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 178 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2003
Details: Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator
RadiationMonochromator: Bent conical Si-mirror (Rh coated) Bent Ge(111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 90638 / % possible obs: 87.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 49.3
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 49.3 / Rsym value: 0.227 / % possible all: 99.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å26.99 Å
Translation2.5 Å26.99 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 2BTL

2btl


Resolution: 1.3→25.42 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.919 / SU B: 1.91 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24612 3256 5.1 %RANDOM
Rwork0.20534 ---
obs0.20737 60751 89.53 %-
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: 17.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0.49 Å2
2--0.13 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.3→25.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 0 175 2392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9242960
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6515261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.323.393112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45715318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0451517
X-RAY DIFFRACTIONr_chiral_restr0.1480.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.021777
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.2927
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.21477
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6890.260
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.9360.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3581.51343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.41322108
X-RAY DIFFRACTIONr_scbond_it6.063999
X-RAY DIFFRACTIONr_scangle_it7.6054.5852
X-RAY DIFFRACTIONr_rigid_bond_restr2.19632342
X-RAY DIFFRACTIONr_sphericity_free3.2553465
X-RAY DIFFRACTIONr_sphericity_bonded2.25132118
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 862 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL1.120.5
MEDIUM THERMAL1.22
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 187 -
Rwork0.281 2856 -
obs--58.09 %

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