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

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Basic information

Entry
Database: PDB / ID: 4xza
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: 1.8 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
Water12,160675
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-14 kcal/mol
Surface area29080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.078, 104.286, 70.538
Angle α, β, γ (deg.)90.00, 92.38, 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: head domain (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.: 675 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 1% Tryptone,0.05M HEPES,20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 61401 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 14.76

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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: 1.8→46.038 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1990 3.24 %
Rwork0.1683 --
obs0.1694 61367 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 0 675 6429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065867
X-RAY DIFFRACTIONf_angle_d0.9927930
X-RAY DIFFRACTIONf_dihedral_angle_d13.9852151
X-RAY DIFFRACTIONf_chiral_restr0.038887
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.8440.26931370.21034206X-RAY DIFFRACTION99
1.844-1.89380.26841510.19774208X-RAY DIFFRACTION100
1.8938-1.94960.23741410.19474267X-RAY DIFFRACTION100
1.9496-2.01250.22571480.17964279X-RAY DIFFRACTION100
2.0125-2.08440.23861370.17644245X-RAY DIFFRACTION100
2.0844-2.16790.23951420.18194226X-RAY DIFFRACTION100
2.1679-2.26650.23661350.17554251X-RAY DIFFRACTION100
2.2665-2.3860.23251470.17524253X-RAY DIFFRACTION100
2.386-2.53550.20361440.17944285X-RAY DIFFRACTION100
2.5355-2.73120.20441430.17364251X-RAY DIFFRACTION100
2.7312-3.00610.2241460.17614253X-RAY DIFFRACTION100
3.0061-3.44090.21481410.16474274X-RAY DIFFRACTION100
3.4409-4.33470.16071390.14754143X-RAY DIFFRACTION97
4.3347-46.05340.16591390.15674236X-RAY DIFFRACTION98

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