[English] 日本語
Yorodumi
- PDB-6l4c: Crystal structure of vicilin from Corylus avellana (Hazelnut) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l4c
TitleCrystal structure of vicilin from Corylus avellana (Hazelnut)
Components48-kDa glycoprotein
KeywordsPLANT PROTEIN / plant seed protein / copper binding protein / electrostatic loop / superoxide dismutase activity
Function / homology
Function and homology information


extraorganismal space / nutrient reservoir activity / protein hexamerization / protein homotrimerization / copper ion binding
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Vicilin Cor a 11.0101
Similarity search - Component
Biological speciesCorylus avellana (European hazelnut)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.191 Å
AuthorsShikhi, M. / Salunke, D.M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Comparative study of 7S globulin from Corylus avellana and Solanum lycopersicum revealed importance of salicylic acid and Cu-binding loop in modulating their function.
Authors: Shikhi, M. / Jain, A. / Salunke, D.M.
History
DepositionOct 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 48-kDa glycoprotein
B: 48-kDa glycoprotein
C: 48-kDa glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,0036
Polymers143,8133
Non-polymers1913
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14300 Å2
ΔGint-126 kcal/mol
Surface area41180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.000, 91.137, 266.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 48-kDa glycoprotein / Vicilin / 7S globulin / Cor a11


Mass: 47937.500 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Corylus avellana (European hazelnut) / References: UniProt: Q8S4P9
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole pH 7.0, 10% w/v Polyethylene glycol 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. obs: 26851 / % possible obs: 98.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 24.3
Reflection shellResolution: 3.19→3.26 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.23 / Num. unique obs: 2595 / % possible all: 95

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER1.12phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEJ

4lej


Resolution: 3.191→43.123 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 1292 4.83 %RANDOM
Rwork0.2265 ---
obs0.2293 26747 98.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.191→43.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8622 0 3 0 8625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028823
X-RAY DIFFRACTIONf_angle_d0.50211903
X-RAY DIFFRACTIONf_dihedral_angle_d14.0995315
X-RAY DIFFRACTIONf_chiral_restr0.0441255
X-RAY DIFFRACTIONf_plane_restr0.0041593
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1908-3.31850.36741150.29122748X-RAY DIFFRACTION96
3.3185-3.46950.32371510.2672802X-RAY DIFFRACTION99
3.4695-3.65230.30641500.26442825X-RAY DIFFRACTION99
3.6523-3.8810.28041410.23992810X-RAY DIFFRACTION99
3.881-4.18040.26651420.22752810X-RAY DIFFRACTION99
4.1804-4.60070.27391530.19052817X-RAY DIFFRACTION98
4.6007-5.26540.24811470.20112811X-RAY DIFFRACTION98
5.2654-6.62990.28791560.23452850X-RAY DIFFRACTION98
6.6299-43.12720.28591370.22152982X-RAY DIFFRACTION97

+
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