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- PDB-9is2: Unheat-treated beta-conglycinin -

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Basic information

Entry
Database: PDB / ID: 9is2
TitleUnheat-treated beta-conglycinin
ComponentsBeta-conglycinin beta subunit 2
KeywordsPLANT PROTEIN / beta-conglycinin / glycoprotein
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: 2.78 Å
AuthorsZhang, T. / Li, J.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2022CXGC010602 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
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14730 Å2
ΔGint-86 kcal/mol
Surface area40400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.019, 63.097, 121.850
Angle α, β, γ (deg.)90.000, 91.310, 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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O
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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 11% PEG4000, 0.1M Sodium Chloride, 0.1M Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2023
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.78→42.11 Å / Num. obs: 66251 / % possible obs: 99.67 % / Redundancy: 1.34 % / Biso Wilson estimate: 29.55 Å2 / CC1/2: 0.964 / Net I/σ(I): 4.2
Reflection shellResolution: 2.78→2.82 Å / Num. unique obs: 66251 / CC1/2: 0.964

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
HKL-30007.21data reduction
PDB_EXTRACT3.27data extraction
PHASER2.7.0phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→42.11 Å / SU ML: 0.4163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.3475
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3248 3830 5.78 %
Rwork0.2443 62421 -
obs0.249 66251 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.77 Å2
Refinement stepCycle: LAST / Resolution: 2.78→42.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8985 0 0 63 9048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00899159
X-RAY DIFFRACTIONf_angle_d1.126112387
X-RAY DIFFRACTIONf_chiral_restr0.06121350
X-RAY DIFFRACTIONf_plane_restr0.00941671
X-RAY DIFFRACTIONf_dihedral_angle_d6.46411209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.820.45621300.33942259X-RAY DIFFRACTION98.96
2.82-2.850.3761360.32712365X-RAY DIFFRACTION98.66
2.85-2.890.39971450.31552270X-RAY DIFFRACTION98.65
2.89-2.930.33931400.31922271X-RAY DIFFRACTION98.89
2.93-2.980.41531430.31252350X-RAY DIFFRACTION98.93
2.98-3.020.3391310.29422328X-RAY DIFFRACTION99.03
3.02-3.070.43481640.29842236X-RAY DIFFRACTION99.3
3.07-3.130.40781280.29922339X-RAY DIFFRACTION98.76
3.13-3.180.3891700.2982299X-RAY DIFFRACTION98.92
3.18-3.240.39851350.2852292X-RAY DIFFRACTION99.47
3.24-3.310.38671520.27792385X-RAY DIFFRACTION99.61
3.31-3.380.37481280.26272245X-RAY DIFFRACTION99.21
3.38-3.460.29891450.26762294X-RAY DIFFRACTION99.63
3.46-3.550.31781340.2522380X-RAY DIFFRACTION99.8
3.55-3.640.3681440.23742297X-RAY DIFFRACTION99.75
3.64-3.750.38521430.24722314X-RAY DIFFRACTION99.8
3.75-3.870.33491400.23662319X-RAY DIFFRACTION99.59
3.87-4.010.32751480.23032307X-RAY DIFFRACTION99.88
4.01-4.170.32431400.22982370X-RAY DIFFRACTION99.8
4.17-4.360.35311350.22182323X-RAY DIFFRACTION99.92
4.36-4.590.25261500.20142307X-RAY DIFFRACTION99.96
4.59-4.870.23521460.18372324X-RAY DIFFRACTION99.84
4.88-5.250.24791440.20432318X-RAY DIFFRACTION99.07
5.25-5.780.28951450.22182302X-RAY DIFFRACTION99.84
5.78-6.610.27271390.22492300X-RAY DIFFRACTION99.59
6.61-8.320.25791410.21232317X-RAY DIFFRACTION99.27
8.32-42.110.2341340.18382310X-RAY DIFFRACTION98.63

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