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- PDB-5e04: Crystal structure of Andes virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 50000
TitleCrystal structure of Andes virus nucleoprotein
ComponentsNucleoprotein
KeywordsNUCLEAR PROTEIN / hantavirus / andes virus / nucleoprotein
Function / homology
Function and homology information


: / viral nucleocapsid / endonuclease activity / host cell Golgi apparatus / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host innate immune response / ribonucleoprotein complex / RNA binding
Similarity search - Function
Hantavirus nucleocapsid protein / Hantavirus nucleocapsid protein
Similarity search - Domain/homology
Biological speciesAndes virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)64,1262
Polymers64,1262
Non-polymers00
Water1,65792
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)32,0631
Polymers32,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)32,0631
Polymers32,0631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.526, 99.652, 136.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein


Mass: 32063.227 Da / Num. of mol.: 2 / Fragment: UNP residues 117-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Andes virus / Production host: Escherichia coli (E. coli) / References: UniProt: O36307
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 100mM HEPES (pH 7.5), 200mM L-proline and 10%(w/v) PEG3350

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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: May 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 33842 / % possible obs: 90.8 % / Redundancy: 6.1 % / Net I/σ(I): 23.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 5000000 / Resolution: 2.25→49.017 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1998 5.92 %
Rwork0.2155 --
obs0.2178 33764 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→49.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 0 92 4436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084453
X-RAY DIFFRACTIONf_angle_d1.2116009
X-RAY DIFFRACTIONf_dihedral_angle_d15.5181657
X-RAY DIFFRACTIONf_chiral_restr0.043663
X-RAY DIFFRACTIONf_plane_restr0.006760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2485-2.30480.30891150.26351824X-RAY DIFFRACTION80
2.3048-2.36710.34241260.26922007X-RAY DIFFRACTION87
2.3671-2.43670.31731330.25852111X-RAY DIFFRACTION92
2.4367-2.51540.32221420.25542262X-RAY DIFFRACTION97
2.5154-2.60530.3011440.24382301X-RAY DIFFRACTION100
2.6053-2.70960.29361460.24152309X-RAY DIFFRACTION100
2.7096-2.83290.32411460.24912315X-RAY DIFFRACTION100
2.8329-2.98220.3211460.24652328X-RAY DIFFRACTION100
2.9822-3.1690.27741480.25322340X-RAY DIFFRACTION100
3.169-3.41370.26011460.22992331X-RAY DIFFRACTION100
3.4137-3.75710.26531500.22132375X-RAY DIFFRACTION100
3.7571-4.30040.22711480.19212354X-RAY DIFFRACTION100
4.3004-5.4170.2021490.18672391X-RAY DIFFRACTION100
5.417-49.02820.20551590.18282518X-RAY DIFFRACTION100

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