[English] 日本語
Yorodumi
- PDB-1fxz: CRYSTAL STRUCTURE OF SOYBEAN PROGLYCININ A1AB1B HOMOTRIMER -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fxz
TitleCRYSTAL STRUCTURE OF SOYBEAN PROGLYCININ A1AB1B HOMOTRIMER
ComponentsGLYCININ G1
KeywordsPLANT PROTEIN / Proglycinin / Glycinin / Legumin / Seed Storage Protein
Function / homology
Function and homology information


protein storage vacuole / nutrient reservoir activity / endoplasmic reticulum
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / 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
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAdachi, M. / Takenaka, Y. / Gidamis, A.B. / Mikami, B. / Utsumi, S.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure of soybean proglycinin A1aB1b homotrimer.
Authors: Adachi, M. / Takenaka, Y. / Gidamis, A.B. / Mikami, B. / Utsumi, S.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and preliminary X-ray Crystallographic analysis of the soybean proglycinin expressed in Escherichia coli.
Authors: Utsumi, S. / Gidamis, A.B. / Mikami, B. / Kito, M.
#2: Journal: Gene / Year: 1988
Title: Signal sequence of preproglycinin affects production of the expressed protein in Escherichia coli.
Authors: Utsumi, S. / Kim, C.S. / Sato, T. / Kito, M.
#3: Journal: J.Agric.Food Chem. / Year: 1987
Title: An alternate cDNA encoding glycinin A1aBx subunit
Authors: Utsumi, S. / Kohno, T. / Mori, T. / Kito, M.
History
DepositionSep 28, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLYCININ G1
B: GLYCININ G1
C: GLYCININ G1


Theoretical massNumber of molelcules
Total (without water)161,0483
Polymers161,0483
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16070 Å2
ΔGint-98 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.524, 115.524, 146.998
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is a trimer corresponding to that in asymmetric unit.

-
Components

#1: Protein GLYCININ G1


Mass: 53682.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Tissue: SEED / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / References: UniProt: P04776
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 302 K / Method: dialysis / pH: 7.6 / Details: pH 7.6, Dialysis, temperature 302.0K
Crystal grow
*PLUS
Temperature: 281 K / pH: 5.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
28 %PEG60001reservoir
30.1 MMES1reservoir
40.4 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 68 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Jan 17, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 142631 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Redundancy: 3.1 %
Reflection
*PLUS
Lowest resolution: 9999 Å / Num. obs: 46010 / Num. measured all: 142631 / Rmerge(I) obs: 0.089

-
Processing

Software
NameVersionClassification
SADIEdata collection
SAINTdata reduction
PHASESphasing
X-PLOR3.1refinement
SADIEdata reduction
SAINTdata scaling
RefinementResolution: 2.8→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.25 2825
Rwork0.199 -
all-35286
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8739 0 0 34 8773
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.199 / Rfactor Rfree: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg3.27
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / Rfactor Rfree: 0.341 / Rfactor obs: 0.271

+
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