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- PDB-3t4r: Lettuce Necrotic Yellow Virus Phosphoprotein C-Terminal Domain -

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Basic information

Entry
Database: PDB / ID: 3t4r
TitleLettuce Necrotic Yellow Virus Phosphoprotein C-Terminal Domain
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Helical bundle / Nucleoprotein
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1590 / : / Lettuce necrotic yellow virus phosphoprotein C-terminal domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / virion component / host cell cytoplasm / Up-down Bundle / Mainly Alpha / Phosphoprotein
Function and homology information
Biological speciesLettuce necrotic yellows virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMartinez, N. / Tarbouriech, N. / Jamin, M.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of the C-terminal domain of lettuce necrotic yellows virus phosphoprotein.
Authors: Martinez, N. / Ribeiro, E.A. / Leyrat, C. / Tarbouriech, N. / Ruigrok, R.W. / Jamin, M.
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,5802
Polymers9,5551
Non-polymers241
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.280, 43.280, 89.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-82-

MG

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Components

#1: Protein Phosphoprotein / Protein P / Protein 4a


Mass: 9555.391 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lettuce necrotic yellows virus / Strain: isolate 318 / Gene: P / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL / References: UniProt: Q9E7N7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.19 Å3/Da / Density % sol: 43.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 50 mM Na Cacodylate, 40 mM Magnesium Acetate, 10% MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.974 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.974 Å / Relative weight: 1
ReflectionResolution: 2→30.6 Å / Num. obs: 6220 / % possible obs: 99.8 % / Redundancy: 10.56 % / Biso Wilson estimate: 43.8 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 20.62
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.88 / Num. unique all: 813 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DNAdata collection
SHELXDphasing
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2→30.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.241 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29351 288 4.6 %RANDOM
Rwork0.22614 ---
all0.22922 ---
obs0.22922 5923 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.189 Å0.188 Å
Refinement stepCycle: LAST / Resolution: 2→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms577 0 1 22 600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.022582
X-RAY DIFFRACTIONr_angle_refined_deg2.0642.001793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.941575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.60626.92326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.88415106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.797151
X-RAY DIFFRACTIONr_chiral_restr0.1430.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021430
X-RAY DIFFRACTIONr_mcbond_it1.0261.5363
X-RAY DIFFRACTIONr_mcangle_it1.7422586
X-RAY DIFFRACTIONr_scbond_it2.9843219
X-RAY DIFFRACTIONr_scangle_it4.5884.5205
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 16 -
Rwork0.29 430 -
obs-813 99.33 %
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)
115.71150.8802-3.63122.8366-0.89499.80710.02820.2866-0.3206-0.3195-0.1878-0.0773-0.2079-0.39790.1595-0.01470.0042-0.01980.18570.00850.06665.57615.60142.215
217.05826.507-4.85415.9722-2.16779.21660.5687-0.98471.4648-0.1393-0.18930.3171-0.87460.227-0.37940.11940.00910.00710.1936-0.04190.14686.86424.85844.987
311.6935-0.43011.059719.9456-2.325711.31740.0775-0.1379-0.9778-0.1937-0.09080.11920.64980.56370.01340.07620.02920.00040.2910.03880.112513.62812.42941.702
419.2671.68956.928717.56094.671918.20560.9593-1.5353-2.60020.594-0.42910.31151.6381-0.5796-0.53020.1608-0.0183-0.09520.5350.27160.326711.0478.59251.403
516.923120.5449.35946.216517.58511.65820.615-0.35750.9386-0.3122-0.9533-0.7335-1.6714-1.11340.33830.5458-0.00140.0580.32360.02370.145922.05227.94551.71
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 17
2X-RAY DIFFRACTION2A18 - 29
3X-RAY DIFFRACTION3A30 - 45
4X-RAY DIFFRACTION4A46 - 59
5X-RAY DIFFRACTION5A60 - 74

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