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- PDB-1uij: Crystal Structure Of Soybean beta-Conglycinin Beta Homotrimer (I1... -

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Basic information

Entry
Database: PDB / ID: 1uij
TitleCrystal Structure Of Soybean beta-Conglycinin Beta Homotrimer (I122M/K124W)
Componentsbeta subunit of beta conglycinin
KeywordsSUGAR BINDING PROTEIN / double-stranded beta helix / seed storage protein
Function / homology
Function and homology information


aleurone grain / protein storage vacuole / nutrient reservoir activity / endoplasmic reticulum
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-conglycinin beta subunit 1
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMaruyama, N. / Maruyama, Y. / Tsuruki, T. / Okuda, E. / Yoshikawa, M. / Utsumi, S.
CitationJournal: BIOCHIM.BIOPHYS.ACTA / Year: 2003
Title: Creation of soybean beta-conglycinin beta with strong phagocytosis-stimulating activity
Authors: Maruyama, N. / Maruyama, Y. / Tsuruki, T. / Okuda, E. / Yoshikawa, M. / Utsumi, S.
History
DepositionJul 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: beta subunit of beta conglycinin
B: beta subunit of beta conglycinin
C: beta subunit of beta conglycinin
D: beta subunit of beta conglycinin
E: beta subunit of beta conglycinin
F: beta subunit of beta conglycinin


Theoretical massNumber of molelcules
Total (without water)288,6516
Polymers288,6516
Non-polymers00
Water4,810267
1
A: beta subunit of beta conglycinin
B: beta subunit of beta conglycinin
C: beta subunit of beta conglycinin


Theoretical massNumber of molelcules
Total (without water)144,3263
Polymers144,3263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-82 kcal/mol
Surface area38290 Å2
MethodPISA
2
D: beta subunit of beta conglycinin
E: beta subunit of beta conglycinin
F: beta subunit of beta conglycinin


Theoretical massNumber of molelcules
Total (without water)144,3263
Polymers144,3263
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14760 Å2
ΔGint-88 kcal/mol
Surface area38230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.263, 62.583, 159.009
Angle α, β, γ (deg.)90.00, 90.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
beta subunit of beta conglycinin / seed storage protein


Mass: 48108.562 Da / Num. of mol.: 6 / Mutation: I122M/K124W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Plasmid: pET21d / Production host: Escherichia coli (E. coli) / References: UniProt: P25974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.44 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 87168 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.2727 -
Rwork0.2208 -
obs-79647
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17866 0 0 267 18133

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