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- PDB-1n93: Crystal Structure of the Borna Disease Virus Nucleoprotein -

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Basic information

Entry
Database: PDB / ID: 1n93
TitleCrystal Structure of the Borna Disease Virus Nucleoprotein
Componentsp40 nucleoprotein
KeywordsVIRAL PROTEIN / RNA virus nucleoprotein tetramer
Function / homology
Function and homology information


: / : / symbiont-mediated arrest of host cell cycle during G2/M transition / helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus
Similarity search - Function
borna disease virus nucleoprotein, domain 1 / borna disease virus nucleoprotein, domain 1 / borna disease virus nucleoprotein, domain 2 / borna disease virus nucleoprotein, domain 2 / P40 nucleoprotein, Borna disease virus / P40 nucleoprotein, subdomain 1, Borna disease virus / P40 nucleoprotein superfamily, Borna disease virus / Borna disease virus P40 protein / P40 nucleoprotein, subdomain 2, Borna disease virus / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoprotein / Nucleoprotein
Similarity search - Component
Biological speciesBorna disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsRudolph, M.G. / Kraus, I. / Dickmanns, A. / Garten, W. / Ficner, R.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of the Borna Disease Virus nucleoprotein
Authors: Rudolph, M.G. / Kraus, I. / Dickmanns, A. / Eickmann, M. / Garten, W. / Ficner, R.
History
DepositionNov 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). The authors state that the crystallographic data strongly support a tetramer. The authors can not confirm this at present, since there are no independent data published as to the oligomeric state of the protein in solution.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: p40 nucleoprotein


Theoretical massNumber of molelcules
Total (without water)41,5101
Polymers41,5101
Non-polymers00
Water5,693316
1
X: p40 nucleoprotein

X: p40 nucleoprotein

X: p40 nucleoprotein

X: p40 nucleoprotein


Theoretical massNumber of molelcules
Total (without water)166,0384
Polymers166,0384
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area19320 Å2
ΔGint-101 kcal/mol
Surface area58130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.026, 100.026, 103.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein p40 nucleoprotein


Mass: 41509.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borna disease virus / Genus: Bornavirus / Plasmid: pMal-c2g / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01552, UniProt: P0C796*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: PEG 550 MME, NaCl, DTT, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
114 mg/mlprotein1drop
220 %PEG550 MME1reservoir
30.1 M1reservoirNaCl
42 mMdithiothreitol1reservoir
50.1 MBicine1reservoirpH9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8841 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8841 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 50437 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 23.87 Å2 / Rsym value: 0.108 / Net I/σ(I): 28
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3 / Num. unique all: 4392 / Rsym value: 0.426 / % possible all: 86.5
Reflection
*PLUS
Lowest resolution: 41.7 Å / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
% possible obs: 86.5 % / Num. unique obs: 4392 / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MAD
Starting model: none

Resolution: 1.76→29.23 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.721 / SU ML: 0.055 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18715 2366 5.1 %RANDOM
Rwork0.16298 ---
obs0.16421 44306 92.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.531 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.76→29.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2586 0 0 316 2902
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212666
X-RAY DIFFRACTIONr_bond_other_d0.0020.022452
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9593608
X-RAY DIFFRACTIONr_angle_other_deg1.53835733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4315333
X-RAY DIFFRACTIONr_chiral_restr0.0890.2413
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022920
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02523
X-RAY DIFFRACTIONr_nbd_refined0.2210.2556
X-RAY DIFFRACTIONr_nbd_other0.2390.22703
X-RAY DIFFRACTIONr_nbtor_other0.1040.21474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.2111
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.228
X-RAY DIFFRACTIONr_mcbond_it1.0551.51671
X-RAY DIFFRACTIONr_mcangle_it1.96922705
X-RAY DIFFRACTIONr_scbond_it2.5383995
X-RAY DIFFRACTIONr_scangle_it4.3044.5903
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.258 157
Rwork0.192 2924
obs-2924
Refinement
*PLUS
Lowest resolution: 29.2 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.34
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg5.43
LS refinement shell
*PLUS
Highest resolution: 1.76 Å / Lowest resolution: 1.81 Å

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