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- PDB-2ca1: Crystal structure of the IBV coronavirus nucleocapsid -

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Basic information

Entry
Database: PDB / ID: 2ca1
TitleCrystal structure of the IBV coronavirus nucleocapsid
ComponentsNUCLEOCAPSID PROTEIN
KeywordsVIRAL PROTEIN / NUCLEOCAPSID PROTEIN / VIRAL NUCLEOPROTEIN
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
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesAVIAN INFECTIOUS BRONCHITIS VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collison, E.W. / Lescar, J. / Prasad, B.V.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. / Collison, E.W. / Lescar, J. / Prasad, B.V.V.
History
DepositionDec 16, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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)25,2772
Polymers25,2772
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.590, 61.590, 91.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.64108, -0.76742, 0.00936), (-0.76711, 0.64034, -0.03885), (0.02382, -0.03208, -0.9992)
Vector: -4.51079, -1.64764, 19.22127)

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Components

#1: Protein NUCLEOCAPSID PROTEIN / INFECTIOUS BRONCHITIS VIRUS NUCLEOCAPSID PROTEIN


Mass: 12638.409 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 218-326
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN INFECTIOUS BRONCHITIS VIRUS / Strain: BEAUDETTE / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q4ZJS4, UniProt: P69596*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHIS-216 AND MET-217 COME FROM CLONING

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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: 3.61 Å3/Da / Density % sol: 65.64 %
Crystal growpH: 8.5 / Details: pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Details: FOCUSING MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→2.7 Å / Num. obs: 31078 / % possible obs: 90.6 % / Observed criterion σ(I): 0 / Redundancy: 1.65 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.23
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 1.66 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.1 / % possible all: 90.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→20 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 447 4.2 %RANDOM
Rwork0.2031 ---
obs0.2031 9388 88.7 %-
Solvent computationBsol: 37.5778 Å2 / ksol: 0.343705 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.814 Å20 Å20 Å2
2---0.814 Å20 Å2
3---1.629 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 0 45 1725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008584
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35201
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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