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- PDB-4qb0: The crystal structure of the C-terminal domain of Ebola (Zaire) n... -

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Basic information

Entry
Database: PDB / ID: 4qb0
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 / MOLECULAR REPLACEMENT / Resolution: 1.75 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
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.599, 49.169, 53.806
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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 1.96 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 19.3% PEG3350, 0.05M Magnesium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2013
RadiationMonochromator: Double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→35 Å / Num. all: 10254 / Num. obs: 9991 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.049 / Net I/σ(I): 31.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.74 / Num. unique all: 403 / Rsym value: 0.292 / % possible all: 82.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→29.359 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2249 489 4.9 %random
Rwork0.183 ---
obs0.185 9989 97.52 %-
all-9991 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→29.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms792 0 0 95 887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013834
X-RAY DIFFRACTIONf_angle_d1.3151134
X-RAY DIFFRACTIONf_dihedral_angle_d13.514306
X-RAY DIFFRACTIONf_chiral_restr0.062110
X-RAY DIFFRACTIONf_plane_restr0.008150
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7504-2.00370.30641440.23932938X-RAY DIFFRACTION93
2.0037-2.52420.25681740.20343200X-RAY DIFFRACTION100
2.5242-29.36270.19721710.16493362X-RAY DIFFRACTION100
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)
14.89310.89140.44465.97010.6644.0820.01110.08340.10240.186-0.02840.0959-0.211-0.24840.0370.15970.01940.02340.19350.00470.117931.991256.814925.3429
22.0012.0606-1.27954.69960.27594.8992-0.19350.0349-0.0292-0.1510.13690.15770.3130.11730.0430.12430.0116-0.01560.15530.00520.149730.285339.406215.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 645 through 684 )
2X-RAY DIFFRACTION2chain 'A' and (resid 685 through 739 )

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