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- PDB-1p65: Crystal structure of the nucleocapsid protein of porcine reproduc... -

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Basic information

Entry
Database: PDB / ID: 1p65
TitleCrystal structure of the nucleocapsid protein of porcine reproductive and respiratory syndrome virus (PRRSV)
Componentsnucleocapsid protein
KeywordsVIRAL PROTEIN / virus / nucleocapsid
Function / homology
Function and homology information


viral nucleocapsid / ribonucleoprotein complex
Similarity search - Function
Helix Hairpins - #90 / Arterivirus nucleocapsid / Arterivirus nucleocapsid protein / Nucleocapsid protein, C-terminal / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Biological speciesPorcine respiratory and reproductive syndrome virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / S-SAD / Resolution: 2.6 Å
AuthorsDoan, D.N.P. / Dokland, T.
Citation
Journal: Structure / Year: 2003
Title: Structure of the nucleocapsid protein of porcine reproductive and respiratory syndrome virus.
Authors: Doan, D.N.P. / Dokland, T.
#1: Journal: To be Published
Title: Cloning, expression, crystallization and preliminary X-ray diffraction analysis of the structural domain of the nucleocapsid N protein from porcine reproductive and respiratory syndrome virus
Authors: Doan, D.N.P. / Dokland, T.
History
DepositionApr 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nucleocapsid protein
B: nucleocapsid protein


Theoretical massNumber of molelcules
Total (without water)16,3442
Polymers16,3442
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-15 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.657, 44.657, 125.347
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein nucleocapsid protein


Mass: 8172.031 Da / Num. of mol.: 2 / Fragment: capsid-forming domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine respiratory and reproductive syndrome virus
Genus: Arterivirus / Gene: orf7 / Plasmid: PET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YJI1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
Conc.: 8 % / Common name: PEG3350 / Details: pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.74 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 27, 2002
RadiationMonochromator: silica / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.74 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 4813 / Num. obs: 4813 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 19.9 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 24.6
Reflection shellResolution: 2.6→2.68 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 12 / Num. unique all: 389 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 389 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: S-SAD / Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.878 / SU B: 11.008 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 0.609 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26659 210 4.5 %RANDOM
Rwork0.20989 ---
all0.2124 4456 --
obs0.2124 4456 100 %-
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: 18.847 Å2
Baniso -1Baniso -2Baniso -3
1-2.81 Å21.4 Å20 Å2
2--2.81 Å20 Å2
3----4.21 Å2
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 0 24 918
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021904
X-RAY DIFFRACTIONr_angle_refined_deg1.7661.9151228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7045112
X-RAY DIFFRACTIONr_chiral_restr0.1290.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02676
X-RAY DIFFRACTIONr_nbd_refined0.2530.2396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2720.241
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.23
X-RAY DIFFRACTIONr_mcbond_it0.6211.5566
X-RAY DIFFRACTIONr_mcangle_it1.1762924
X-RAY DIFFRACTIONr_scbond_it2.1093338
X-RAY DIFFRACTIONr_scangle_it3.544.5304
LS refinement shellResolution: 2.6→2.708 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.278 23
Rwork0.247 493
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)
14.9303-2.92325.65223.4621-2.773814.9435-0.4573-0.3117-0.17550.36040.30110.07990.3873-0.00790.15620.2895-0.08470.04750.05780.02770.21512.776524.939171.3211
25.1378-0.12313.42222.8517-3.764911.6343-0.41650.15110.1427-0.1320.31390.42430.12-0.52870.10260.245-0.1053-0.01170.0455-0.00220.2378-3.24727.215659.6228
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 6712 - 68
2X-RAY DIFFRACTION2BB11 - 6712 - 68
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.77
LS refinement shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.71 Å

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