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- PDB-2c86: x-ray structure of the N and C-terminal domain of coronavirus nuc... -

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Basic information

Entry
Database: PDB / ID: 2c86
Titlex-ray structure of the N and C-terminal domain of coronavirus nucleocapsid protein.
ComponentsNUCLEOCAPSID PROTEIN
KeywordsNUCLEOCAPSID PROTEIN / PHOSPHORYLATION / RNA-BINDING / VIRAL NUCLEOPROTEIN
Function / homology
Function and homology information


viral nucleocapsid / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / ribonucleoprotein complex / RNA binding
Similarity search - Function
Nucleocapsid protein, gammacoronavirus / 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
Biological speciesAVIAN INFECTIOUS BRONCHITIS VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collinson, 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. / Collisson, E.W. / Lescar, J. / Prasad, B.V.V.
History
DepositionDec 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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

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Assembly

Deposited unit
A: NUCLEOCAPSID PROTEIN
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)30,0292
Polymers30,0292
Non-polymers00
Water61334
1
A: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0151
Polymers15,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: NUCLEOCAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)15,0151
Polymers15,0151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.399, 96.662, 66.593
Angle α, β, γ (deg.)90.00, 98.53, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 134
2114B1 - 134

NCS oper: (Code: given
Matrix: (0.37591, -0.92665, 0.00305), (-0.92629, -0.37585, -0.02685), (0.02603, 0.00726, -0.99963)
Vector: 1.56722, -3.17674, 16.0061)

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Components

#1: Protein NUCLEOCAPSID PROTEIN / IBV NUCLEOCAPSID / N STRUCTURAL PROTEIN / NC


Mass: 15014.549 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 29-160 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AVIAN INFECTIOUS BRONCHITIS VIRUS / Strain: BEAUDETTE US / Plasmid: PET16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P69598
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAJOR STRUCTURAL COMPONENT OF VIRIONS ENGINEERED RESIDUE IN CHAIN A, LYS 85 TO CYS ENGINEERED ...MAJOR STRUCTURAL COMPONENT OF VIRIONS ENGINEERED RESIDUE IN CHAIN A, LYS 85 TO CYS ENGINEERED RESIDUE IN CHAIN B, LYS 85 TO CYS

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.4 / Details: 20% PEG 3350, 0.2M LITHIUM SULFATE, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 8739 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.3
Reflection shellResolution: 3→3.16 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.1 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BTL

1btl


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.826 / SU B: 23.676 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.328 413 4.8 %RANDOM
Rwork0.266 ---
obs0.269 8264 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.42 Å2
Baniso -1Baniso -2Baniso -3
1-3.47 Å20 Å2-1.8 Å2
2---5 Å20 Å2
3---0.99 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2130 0 0 34 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222208
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9233000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57423.509114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.78115320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5591516
X-RAY DIFFRACTIONr_chiral_restr0.090.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.21062
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.21438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3030.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2520.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5341.51353
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.97422132
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.71531012
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.0644.5868
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1065 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.470.5
medium thermal0.262
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.447 31
Rwork0.392 573

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