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- PDB-4xz8: The crystal structure of Erve virus nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 4xz8
TitleThe crystal structure of Erve virus nucleoprotein
ComponentsNucleoprotein
KeywordsRNA BINDING PROTEIN / nucleoprotein / Erve virus
Function / homologyNucleocapsid N protein / Nucleocapsid N protein / helical viral capsid / viral nucleocapsid / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesErve virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGuo, Y. / Wang, W. / Liu, X. / Wang, X. / Wang, J. / Huo, T. / Liu, B.
CitationJournal: J.Virol. / Year: 2015
Title: Structural and Functional Diversity of Nairovirus-Encoded Nucleoproteins.
Authors: Wang, W. / Liu, X. / Wang, X. / Dong, H. / Ma, C. / Wang, J. / Liu, B. / Mao, Y. / Wang, Y. / Li, T. / Yang, C. / Guo, Y.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoprotein
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)106,7262
Polymers106,7262
Non-polymers00
Water4,864270
1
A: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,3631
Polymers53,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoprotein


Theoretical massNumber of molelcules
Total (without water)53,3631
Polymers53,3631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.899, 67.895, 154.079
Angle α, β, γ (deg.)90.00, 93.56, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nucleoprotein


Mass: 53362.996 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-482
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erve virus / Production host: Escherichia coli (E. coli) / References: UniProt: J3S7E7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.44 Å3/Da / Density % sol: 49.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 200mM sodium malonate, 20% (wt/vol) PEG 3350,7% (vol/vol) 1-Butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 42902 / % possible obs: 99.3 % / Redundancy: 4.3 % / Net I/σ(I): 9.071

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALEPACKdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U3I

3u3i


Resolution: 2.35→33.454 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 2017 4.7 %
Rwork0.1741 --
obs0.1775 42875 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→33.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7381 0 0 270 7651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087527
X-RAY DIFFRACTIONf_angle_d1.10910173
X-RAY DIFFRACTIONf_dihedral_angle_d15.5782783
X-RAY DIFFRACTIONf_chiral_restr0.0431132
X-RAY DIFFRACTIONf_plane_restr0.0051314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3459-2.40450.2861520.20792769X-RAY DIFFRACTION94
2.4045-2.46950.35121350.20922906X-RAY DIFFRACTION100
2.4695-2.54220.26861420.21882948X-RAY DIFFRACTION100
2.5422-2.62420.32331570.21462945X-RAY DIFFRACTION100
2.6242-2.71790.33291380.22932902X-RAY DIFFRACTION100
2.7179-2.82670.32161450.22292925X-RAY DIFFRACTION100
2.8267-2.95530.30151380.212965X-RAY DIFFRACTION100
2.9553-3.1110.3021490.20442935X-RAY DIFFRACTION100
3.111-3.30570.28621410.19762931X-RAY DIFFRACTION100
3.3057-3.56070.24071470.16932961X-RAY DIFFRACTION100
3.5607-3.91850.21831440.14072922X-RAY DIFFRACTION100
3.9185-4.48440.17771440.13032938X-RAY DIFFRACTION99
4.4844-5.64550.19941450.13822971X-RAY DIFFRACTION99
5.6455-33.45780.20441400.16712840X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 10.1415 Å / Origin y: 11.1974 Å / Origin z: 39.5293 Å
111213212223313233
T0.1425 Å20.0017 Å20.003 Å2-0.1221 Å20.0028 Å2--0.1445 Å2
L0.4914 °20.0636 °20.1376 °2--0.0041 °20.0013 °2--0.2823 °2
S0.0014 Å °0.1616 Å °-0.0494 Å °0.0188 Å °0.0359 Å °-0.0016 Å °-0.0094 Å °-0.0075 Å °0.0012 Å °
Refinement TLS groupSelection details: all

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