[English] 日本語
Yorodumi
- PDB-3t4r: Lettuce Necrotic Yellow Virus Phosphoprotein C-Terminal Domain -

+
Open data


ID or keywords:

Loading...

-
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 / virion component => GO:0044423 / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more