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- PDB-9is0: Ultra-high temperature sterilization-treated beta-conglycinin -

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Basic information

Entry
Database: PDB / ID: 9is0
TitleUltra-high temperature sterilization-treated beta-conglycinin
ComponentsBeta-conglycinin beta subunit 2
KeywordsPLANT PROTEIN / beta-conglycinin beta homotrimers / ultra-high temperature sterilization-treated
Function / homology
Function and homology information


aleurone grain / protein storage vacuole / endoplasmic reticulum
Similarity search - Function
: / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
Beta-conglycinin beta subunit 2
Similarity search - Component
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.23 Å
AuthorsZhang, T. / Li, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other private2022CXGC010602 China
CitationJournal: To Be Published
Title: Characterization and structural analyses of beta-conglycinin after thermal sterilization
Authors: Zhang, T. / Li, J.Y.
History
DepositionJul 16, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Beta-conglycinin beta subunit 2
A: Beta-conglycinin beta subunit 2
B: Beta-conglycinin beta subunit 2


Theoretical massNumber of molelcules
Total (without water)133,4753
Polymers133,4753
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-80 kcal/mol
Surface area41310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.896, 81.880, 86.569
Angle α, β, γ (deg.)90.000, 118.380, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-conglycinin beta subunit 2 / CG-beta-2


Mass: 44491.543 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Gene: CG-4, GLYMA_20G148200 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F7J077
Has protein modificationN

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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: 1.98 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 28% PEG400, 0.05M Magnesium acetate tetrahydrate, 0.05M Sodium acetate
Temp details: Before crystallization, the protein sample was heated at 408.15k for 15s

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.23→28.83 Å / Num. obs: 16327 / % possible obs: 96.31 % / Redundancy: 1.38 % / Biso Wilson estimate: 63.85 Å2 / CC1/2: 0.987 / Net I/σ(I): 4.7
Reflection shellResolution: 3.23→3.32 Å / Num. unique obs: 830 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.23→28.83 Å / SU ML: 0.5279 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.386
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3224 1654 10.13 %
Rwork0.227 14673 -
obs0.2369 16327 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.2 Å2
Refinement stepCycle: LAST / Resolution: 3.23→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8985 0 0 0 8985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01129159
X-RAY DIFFRACTIONf_angle_d1.46612387
X-RAY DIFFRACTIONf_chiral_restr0.07521350
X-RAY DIFFRACTIONf_plane_restr0.01571671
X-RAY DIFFRACTIONf_dihedral_angle_d6.87621209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.23-3.320.3871810.3033830X-RAY DIFFRACTION64.93
3.32-3.430.39641520.28911248X-RAY DIFFRACTION99.08
3.43-3.550.36321410.27281244X-RAY DIFFRACTION99
3.55-3.690.37541380.25491253X-RAY DIFFRACTION99.43
3.69-3.860.34591460.24571251X-RAY DIFFRACTION99.5
3.86-4.060.33381420.22271243X-RAY DIFFRACTION99.35
4.06-4.320.33711340.22731272X-RAY DIFFRACTION99.08
4.32-4.650.33461360.20921257X-RAY DIFFRACTION99.86
4.65-5.120.30831510.2081272X-RAY DIFFRACTION99.37
5.12-5.850.30421470.20541259X-RAY DIFFRACTION99.72
5.85-7.350.31471410.23491276X-RAY DIFFRACTION99.09
7.35-28.830.25471450.19071268X-RAY DIFFRACTION96.98

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