[English] 日本語
Yorodumi
- PDB-4y6x: Structure of Tobacco streak virus coat protein at 2.1 Angstroms r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4y6x
TitleStructure of Tobacco streak virus coat protein at 2.1 Angstroms resolution (C2 crystal form)
ComponentsCoat protein
KeywordsSTRUCTURAL PROTEIN / domain-swapped dimer / jelly roll beta-barrel
Function / homologyCoat protein, Ilarvirus, predicted / Coat protein, Ilarvirus / Ilarvirus coat protein / viral capsid / RNA binding / Coat protein
Function and homology information
Biological speciesTobacco streak virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGulati, A. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
DST, DBT, J.C Bose India
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structural studies on tobacco streak virus coat protein: Insights into the pleomorphic nature of ilarviruses
Authors: Gulati, A. / Alapati, K. / Murthy, A. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionFeb 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)55,6003
Polymers55,6003
Non-polymers00
Water3,423190
1
A: Coat protein

A: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area2720 Å2
ΔGint-21 kcal/mol
Surface area14470 Å2
MethodPISA
2
B: Coat protein

B: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Buried area2640 Å2
ΔGint-24 kcal/mol
Surface area14840 Å2
MethodPISA
3
C: Coat protein

C: Coat protein


Theoretical massNumber of molelcules
Total (without water)37,0672
Polymers37,0672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area2160 Å2
ΔGint-21 kcal/mol
Surface area15270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.580, 74.670, 85.500
Angle α, β, γ (deg.)90.000, 123.730, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNAA90 - 23718 - 165
21GLNGLNBB90 - 23718 - 165
12ASNASNAA90 - 23618 - 164
22ASNASNCC90 - 23618 - 164
13VALVALBB90 - 23518 - 163
23VALVALCC90 - 23518 - 163

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Coat protein


Mass: 18533.301 Da / Num. of mol.: 3 / Fragment: UNP residues 73-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco streak virus / Production host: Escherichia coli (E. coli) / References: UniProt: A7UMQ4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 43.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 24% PEG 1500, 0.2 M L-Proline, 0.1 M HEPES

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.2819 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2013
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2819 Å / Relative weight: 1
ReflectionResolution: 2.1→71.107 Å / Num. all: 27988 / Num. obs: 27988 / % possible obs: 99.8 % / Redundancy: 4.1 % / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Rsym value: 0.067 / Net I/av σ(I): 8.822 / Net I/σ(I): 13.1 / Num. measured all: 114040
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2140.47831608340300.2730.478399.5
2.21-2.354.10.3262.31557938450.1860.3264.299.6
2.35-2.514.10.2373.11483936300.1340.2375.699.8
2.51-2.714.10.164.61371733570.090.167.799.8
2.71-2.974.10.1017.31283431390.0570.10111.4100
2.97-3.324.10.06310.71157028110.0350.06318100
3.32-3.834.10.04514.91023424880.0250.04525.1100
3.83-4.74.10.03816.4875121190.0210.03830.4100
4.7-6.644.10.03716.5681016600.0210.03730.9100
6.64-28.93340.03415.136239090.0190.03431.699

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y6T

4y6t


Resolution: 2.1→28.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.225 / WRfactor Rwork: 0.1755 / FOM work R set: 0.851 / SU B: 4.845 / SU ML: 0.128 / SU R Cruickshank DPI: 0.1981 / SU Rfree: 0.177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 1407 5 %RANDOM
Rwork0.178 ---
obs0.1806 26581 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.64 Å2 / Biso mean: 39.856 Å2 / Biso min: 17.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.1→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3265 0 0 190 3455
Biso mean---45.11 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023342
X-RAY DIFFRACTIONr_bond_other_d0.0070.023216
X-RAY DIFFRACTIONr_angle_refined_deg1.6911.9614549
X-RAY DIFFRACTIONr_angle_other_deg1.3637326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44422.167120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3391526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213751
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02775
X-RAY DIFFRACTIONr_mcbond_it3.8433.8491725
X-RAY DIFFRACTIONr_mcbond_other3.8223.8491724
X-RAY DIFFRACTIONr_mcangle_it5.5345.7462144
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A73000.12
12B73000.12
21A71930.13
22C71930.13
31B70480.13
32C70480.13
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 116 -
Rwork0.247 1924 -
all-2040 -
obs--99.32 %

+
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