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- PDB-5e06: Structure of Sin Nombre virus nucleoprotein in long-axis crystal form -

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Basic information

Entry
Database: PDB / ID: 5000000
TitleStructure of Sin Nombre virus nucleoprotein in long-axis crystal form
ComponentsNucleocapsid protein
KeywordsNUCLEAR PROTEIN / hantavirus / Sin Nombre virus / nucleoprotein
Function / homology
Function and homology information


regulation of translation / host cell Golgi apparatus / viral nucleocapsid / endonuclease activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / hydrolase activity / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesSin Nombre virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.001 Å
AuthorsGuo, Y. / Wang, W.M. / Lou, Z.Y.
CitationJournal: J.Virol. / Year: 2015
Title: Crystal Structure of the Core Region of Hantavirus Nucleocapsid Protein Reveals the Mechanism for Ribonucleoprotein Complex Formation
Authors: Guo, Y. / Wang, W. / Sun, Y. / Ma, C. / Wang, X. / Wang, X. / Liu, P. / Shen, S. / Li, B. / Lin, J. / Deng, F. / Wang, H. / Lou, Z.
History
DepositionSep 28, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)32,1581
Polymers32,1581
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13670 Å2
Unit cell
Length a, b, c (Å)49.329, 49.329, 419.956
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Nucleocapsid protein


Mass: 32158.184 Da / Num. of mol.: 1 / Fragment: UNP residues 112-395
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sin Nombre virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9E1J8, UniProt: Q89462*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 200 mM lithium sulfate monohydrate and 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 7053 / % possible obs: 100 % / Redundancy: 11.8 % / Net I/σ(I): 45

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.001→42.72 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2809 330 4.76 %
Rwork0.224 --
obs0.2267 6937 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.001→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 0 0 2155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012205
X-RAY DIFFRACTIONf_angle_d1.2892982
X-RAY DIFFRACTIONf_dihedral_angle_d15.874820
X-RAY DIFFRACTIONf_chiral_restr0.046328
X-RAY DIFFRACTIONf_plane_restr0.005382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0012-3.78080.29231640.2193166X-RAY DIFFRACTION100
3.7808-42.72450.27631660.22593441X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.2379 Å / Origin y: -10.6394 Å / Origin z: -16.0217 Å
111213212223313233
T0.6815 Å2-0.089 Å2-0.0424 Å2-0.44 Å20.118 Å2--0.6315 Å2
L2.563 °2-0.1297 °2-0.7847 °2-1.5348 °2-0.857 °2--2.6378 °2
S-0.0228 Å °-0.4879 Å °-0.2505 Å °0.4223 Å °0.0515 Å °-0.2036 Å °0.084 Å °0.3083 Å °0.0015 Å °
Refinement TLS groupSelection details: chain A

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