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- PDB-4z9p: Crystal structure of Ebola virus nucleoprotein core domain at 1.8... -

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Basic information

Entry
Database: PDB / ID: 4z9p
TitleCrystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / Ebola / Filoviridae / nucleoprotein / RNA binding protein
Function / homologyEbola nucleoprotein / Ebola nucleoprotein / viral RNA genome packaging / helical viral capsid / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA binding / Nucleoprotein
Function and homology information
Biological speciesZaire ebolavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.792 Å
AuthorsGuo, Y. / Dong, S.S. / Yang, P. / Li, G.B. / Liu, B.C. / Yang, C. / Rao, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31300606 China
CitationJournal: Protein Cell / Year: 2015
Title: Insight into the Ebola virus nucleocapsid assembly mechanism: crystal structure of Ebola virus nucleoprotein core domain at 1.8 A resolution.
Authors: Dong, S. / Yang, P. / Li, G. / Liu, B. / Wang, W. / Liu, X. / Xia, B. / Yang, C. / Lou, Z. / Guo, Y. / Rao, Z.
History
DepositionApr 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2015Group: Data collection
Revision 1.2Oct 18, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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


Theoretical massNumber of molelcules
Total (without water)35,1281
Polymers35,1281
Non-polymers00
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.845, 162.877, 31.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Protein Nucleoprotein / / Nucleocapsid protein / Protein N


Mass: 35128.465 Da / Num. of mol.: 1 / Fragment: core domain (UNP RESIDUES 36-351)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus (strain Mayinga-76) / Strain: Mayinga-76 / Gene: NP / Production host: Escherichia coli (E. coli) / References: UniProt: P18272
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.31 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 7
Details: 200mM ammonium citrate tribasic pH 7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97848 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 1.792→50 Å / Num. obs: 29588 / % possible obs: 99.8 % / Redundancy: 10.6 % / Biso Wilson estimate: 27.12 Å2 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Rrim(I) all: 0.088 / Χ2: 2.425 / Net I/av σ(I): 35.444 / Net I/σ(I): 6.7 / Num. measured all: 312835
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.83100.54614770.90.1790.5750.48499.9
1.83-1.86110.46814200.9380.1450.4910.51299.8
1.86-1.910.90.44514270.950.1390.4670.53399.9
1.9-1.9410.70.50814690.9210.1630.5351.266100
1.94-1.9810.80.32314610.9680.1020.3390.58899.9
1.98-2.0310.70.24714300.9780.0780.2590.63999.9
2.03-2.0810.50.20514850.9840.0660.2150.76100
2.08-2.1310.30.17514490.9860.0570.1850.8399.7
2.13-2.29.80.16314420.9870.0540.1721.04999.9
2.2-2.2710.40.19414830.9720.0630.2041.60899.9
2.27-2.3511.20.14414430.990.0450.1511.166100
2.35-2.4410.90.11514800.9930.0360.1211.22199.9
2.44-2.5511.10.10914620.9810.0340.1141.67999.9
2.55-2.6910.60.114870.9940.0320.1051.86499.9
2.69-2.869.90.09415030.9920.0310.12.699.8
2.86-3.0811.40.08714800.9950.0270.0912.459100
3.08-3.3911.10.07814940.9910.0250.0823.27499.9
3.39-3.88100.06614940.9970.0220.073.91198.5
3.88-4.8810.20.05415380.9950.0180.0574.80799.8
4.88-509.90.06416640.9890.0220.06816.42199.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.792→40.719 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 1472 4.99 %
Rwork0.1906 28020 -
obs0.1923 29492 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 39.5676 Å2 / Biso min: 12.74 Å2
Refinement stepCycle: final / Resolution: 1.792→40.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 211 2512
Biso mean---45.79 -
Num. residues----293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072341
X-RAY DIFFRACTIONf_angle_d0.9783154
X-RAY DIFFRACTIONf_chiral_restr0.044359
X-RAY DIFFRACTIONf_plane_restr0.004405
X-RAY DIFFRACTIONf_dihedral_angle_d15.232858
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7922-1.85010.31191310.23252346247793
1.8501-1.91620.30991410.262524962637100
1.9162-1.99290.28371360.250325242660100
1.9929-2.08360.24051130.192825512664100
2.0836-2.19350.23591530.185124922645100
2.1935-2.33090.25141160.211225582674100
2.3309-2.51080.23551440.185125402684100
2.5108-2.76350.22921260.190225722698100
2.7635-3.16320.23021290.202726102739100
3.1632-3.98480.22391240.17342610273499
3.9848-40.72970.19011590.17582721288099
Refinement TLS params.Method: refined / Origin x: 15.9015 Å / Origin y: 21.3565 Å / Origin z: 4.2416 Å
111213212223313233
T0.1795 Å2-0.0012 Å2-0.0193 Å2-0.1913 Å2-0.0138 Å2--0.1251 Å2
L2.7176 °20.6181 °2-0.1114 °2-1.9488 °2-0.1555 °2--0.6978 °2
S-0.0369 Å °0.1342 Å °-0.2547 Å °-0.1271 Å °-0.0017 Å °0.0217 Å °0.0431 Å °0.0462 Å °0.018 Å °
Refinement TLS groupSelection details: ALL

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