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- PDB-3lq6: Crystal Structure of Murine Norovirus Protruding (P) Domain -

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Basic information

Entry
Database: PDB / ID: 3lq6
TitleCrystal Structure of Murine Norovirus Protruding (P) Domain
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / Viral capsid protein / protruding (P) domain
Function / homology
Function and homology information


virus-mediated perturbation of host defense response
Similarity search - Function
Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRubin, J.R. / Stuckey, J.A.
CitationJournal: J.Virol. / Year: 2010
Title: High-resolution x-ray structure and functional analysis of the murine norovirus 1 capsid protein protruding domain.
Authors: Taube, S. / Rubin, J.R. / Katpally, U. / Smith, T.J. / Kendall, A. / Stuckey, J.A. / Wobus, C.E.
History
DepositionFeb 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Capsid protein
B: Capsid protein


Theoretical massNumber of molelcules
Total (without water)69,7172
Polymers69,7172
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-13 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.800, 86.326, 83.543
Angle α, β, γ (deg.)90.00, 110.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein


Mass: 34858.281 Da / Num. of mol.: 2 / Fragment: Protruding (P) Domain, residues 228-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Strain: MNV-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2V8W4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 20% PEG 3350, 0.2 M Sodium Acetate, 90 mM glycine, 10 mM sodium chloride, 10 mM Tris, 0.5 mM dithiothreitol, , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49163 / % possible obs: 90.4 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.078 / Net I/σ(I): 10
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2 / % possible all: 71

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2OBR

2obr


Resolution: 2→35.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.539 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2597 5.1 %RANDOM
Rwork0.189 ---
obs0.191 48254 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.17 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→35.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4808 0 0 256 5064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0224932
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9716750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8595624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48123.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33515730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1071532
X-RAY DIFFRACTIONr_chiral_restr0.1580.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0223822
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.53122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.31625050
X-RAY DIFFRACTIONr_scbond_it3.23131810
X-RAY DIFFRACTIONr_scangle_it5.0144.51700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 183 -
Rwork0.231 3455 -
obs--96.83 %

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