[English] 日本語
Yorodumi
- PDB-2cv6: Crystal Structure of 8Salpha Globulin, the Major Seed Storage Pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2cv6
TitleCrystal Structure of 8Salpha Globulin, the Major Seed Storage Protein of Mungbean
ComponentsSeed storage protein
KeywordsPLANT PROTEIN / cupin
Function / homology
Function and homology information


nutrient reservoir activity
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
8S globulin alpha isoform
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsItoh, T. / Garcia, R.N. / Adachi, M. / Maruyama, Y. / Tecson-Mendoza, E.M. / Mikami, B. / Utsumi, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of 8Salpha globulin, the major seed storage protein of mung bean.
Authors: Itoh, T. / Garcia, R.N. / Adachi, M. / Maruyama, Y. / Tecson-Mendoza, E.M. / Mikami, B. / Utsumi, S.
History
DepositionMay 31, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Seed storage protein


Theoretical massNumber of molelcules
Total (without water)48,7311
Polymers48,7311
Non-polymers00
Water1448
1
A: Seed storage protein

A: Seed storage protein

A: Seed storage protein


Theoretical massNumber of molelcules
Total (without water)146,1943
Polymers146,1943
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15690 Å2
ΔGint-107 kcal/mol
Surface area39790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)146.600, 146.600, 53.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a trimer.

-
Components

#1: Protein Seed storage protein


Mass: 48731.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / References: UniProt: Q198W5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1000, NaCl, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.61→37 Å / Num. all: 33649 / Num. obs: 11640 / % possible obs: 89.6 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 38.7 Å2
Reflection shellResolution: 2.61→2.71 Å / % possible all: 71

-
Processing

Software
NameVersionClassification
CNS1.1refinement
SADIEdata reduction
SAINTdata reduction
SAINTdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→9.99 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 531730.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CRYST1 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL OBVERSE SETTING
RfactorNum. reflection% reflectionSelection details
Rfree0.258 560 5.2 %RANDOM
Rwork0.196 ---
obs0.196 10853 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2037 Å2 / ksol: 0.331602 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1--16.89 Å2-0.25 Å20 Å2
2---16.89 Å20 Å2
3---33.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.65→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2976 0 0 8 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.192
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 2.65→2.81 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.43 79 5.4 %
Rwork0.356 1379 -
obs--71.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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