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- PDB-4qaz: The crystal structure of the C-terminal domain of Ebola (Zaire) n... -

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Basic information

Entry
Database: PDB / ID: 4qaz
TitleThe crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
ComponentsNucleoprotein
KeywordsVIRAL PROTEIN / new family / Ebola virus VP40
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 speciesEbola virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å
AuthorsDerewenda, U. / Dziubanska, P.J. / Derewenda, Z.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The structure of the C-terminal domain of the Zaire ebolavirus nucleoprotein.
Authors: Dziubanska, P.J. / Derewenda, U. / Ellena, J.F. / Engel, D.A. / Derewenda, Z.S.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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)12,3401
Polymers12,3401
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.515, 56.515, 63.546
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-836-

HOH

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Components

#1: Protein Nucleoprotein / Nucleocapsid protein / Protein N


Mass: 12339.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Strain: Mayinga / Gene: NP / Plasmid: Parallel1-MBPHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P18272
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 19.3% PEG3350, 0.3M Magnesium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97907 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.98→35 Å / Num. all: 8699 / Num. obs: 8428 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.125 / Net I/σ(I): 12.5
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 325 / Rsym value: 0.262 / % possible all: 76.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
SHELXEmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.98→26.65 Å / SU ML: 0.17 / σ(F): 1.15 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 729 4.71 %random
Rwork0.1839 ---
all0.1859 8428 --
obs0.1859 8427 95.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→26.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms790 0 0 100 890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012830
X-RAY DIFFRACTIONf_angle_d1.31127
X-RAY DIFFRACTIONf_dihedral_angle_d14.593308
X-RAY DIFFRACTIONf_chiral_restr0.058111
X-RAY DIFFRACTIONf_plane_restr0.007146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9672-2.1190.25931360.21552508X-RAY DIFFRACTION82
2.119-2.33220.23061490.19933063X-RAY DIFFRACTION100
2.3322-2.66940.25051620.19743068X-RAY DIFFRACTION100
2.6694-3.36210.22631480.19813061X-RAY DIFFRACTION100
3.3621-26.65230.22091340.16993059X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.20111.64040.04547.1608-1.632.16330.0469-0.21820.26450.574-0.10890.6444-0.3056-0.50950.01530.29570.05680.04550.3816-0.07280.324114.64650.35050.2454
22.82780.93390.60557.4847-0.88942.5851-0.1145-0.1534-0.0611-0.23680.26490.59590.3263-0.3242-0.10510.2895-0.0441-0.01140.40890.0070.313113.0003-18.4598-4.1656
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 645 through 693 )
2X-RAY DIFFRACTION2chain 'A' and (resid 694 through 739 )

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