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- PDB-2c86: x-ray structure of the N and C-terminal domain of coronavirus nuc... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c86 | ||||||
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Title | x-ray structure of the N and C-terminal domain of coronavirus nucleocapsid protein. | ||||||
![]() | NUCLEOCAPSID PROTEIN | ||||||
![]() | NUCLEOCAPSID PROTEIN / PHOSPHORYLATION / RNA-BINDING / VIRAL NUCLEOPROTEIN | ||||||
Function / homology | ![]() host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / RNA binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Jayaram, H. / Fan, H. / Bowman, B.R. / Ooi, A. / Jayaram, J. / Collinson, E.W. / Lescar, J. / Prasad, B.V.V. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 48.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.1 KB | Display | ![]() |
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Full document | ![]() | 442.7 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ca1C ![]() 2ge7C ![]() 2ge8C ![]() 2gecC ![]() 1btlS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (0.37591, -0.92665, 0.00305), Vector: |
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Components
#1: Protein | 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.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | MAJOR STRUCTURAL COMPONENT OF VIRIONS ENGINEERED RESIDUE IN CHAIN A, LYS 85 TO CYS ENGINEERED ...MAJOR STRUCTURAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50 % |
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Crystal grow | pH: 7.4 / Details: 20% PEG 3350, 0.2M LITHIUM SULFATE, pH 7.40 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57.42 Å2
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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