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- PDB-9is1: Pasteurization-treated beta-conglycinin -

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Basic information

Entry
Database: PDB / ID: 9is1
TitlePasteurization-treated beta-conglycinin
ComponentsBeta-conglycinin beta subunit 2
KeywordsPLANT PROTEIN / beta-conglycinin / beta homotrimers
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: 2.01 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: Li, J.Y. / Zhang, T.
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
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15120 Å2
ΔGint-82 kcal/mol
Surface area40000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.110, 83.460, 86.920
Angle α, β, γ (deg.)90.000, 118.360, 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.: 476 / 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: 2.14 Å3/Da / Density % sol: 42.48 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 22% PEG400, 0.1M Magnesium Chloride hexahydrate, 0.1M Tris
Temp details: Before crystallization, the protein sample was heated to 353.15K for 30S

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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: 2.01→37.45 Å / Num. obs: 125347 / % possible obs: 96.02 % / Redundancy: 1.34 % / Biso Wilson estimate: 27.46 Å2 / CC1/2: 0.474 / Net I/σ(I): 4.4
Reflection shellResolution: 2.01→2.04 Å / Num. unique obs: 4393 / CC1/2: 0.474

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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: 2.01→37.45 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.9522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2945 3682 2.94 %
Rwork0.2442 121665 -
obs0.2457 125347 89.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.51 Å2
Refinement stepCycle: LAST / Resolution: 2.01→37.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8985 0 0 476 9461
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00889159
X-RAY DIFFRACTIONf_angle_d1.104612387
X-RAY DIFFRACTIONf_chiral_restr0.0621350
X-RAY DIFFRACTIONf_plane_restr0.00971671
X-RAY DIFFRACTIONf_dihedral_angle_d6.66861209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.040.37791530.3264393X-RAY DIFFRACTION84.48
2.04-2.060.36391170.34084207X-RAY DIFFRACTION80.67
2.06-2.090.45281110.39153937X-RAY DIFFRACTION74.81
2.09-2.130.46721310.34814684X-RAY DIFFRACTION88.46
2.13-2.160.30231530.33184653X-RAY DIFFRACTION90.07
2.16-2.190.40231270.3334769X-RAY DIFFRACTION90.03
2.19-2.230.44021410.36274446X-RAY DIFFRACTION85.82
2.23-2.270.5487710.45352609X-RAY DIFFRACTION49.71
2.27-2.320.40991580.37654429X-RAY DIFFRACTION84.68
2.32-2.360.33671550.29844908X-RAY DIFFRACTION94.28
2.36-2.410.34531460.27965060X-RAY DIFFRACTION96.35
2.41-2.470.31961430.27285065X-RAY DIFFRACTION96.73
2.47-2.530.26551430.26025082X-RAY DIFFRACTION96.87
2.53-2.60.31611740.27145058X-RAY DIFFRACTION96.8
2.6-2.680.38571490.28864724X-RAY DIFFRACTION90.83
2.68-2.760.33311430.28234885X-RAY DIFFRACTION93.09
2.76-2.860.32451500.25365009X-RAY DIFFRACTION96.83
2.86-2.980.23711620.23685132X-RAY DIFFRACTION97.82
2.98-3.110.2791530.23255145X-RAY DIFFRACTION97.66
3.11-3.280.26211490.22665085X-RAY DIFFRACTION97.38
3.28-3.480.28541450.2154699X-RAY DIFFRACTION89.75
3.48-3.750.26911280.21774371X-RAY DIFFRACTION84.05
3.75-4.130.24751370.20134533X-RAY DIFFRACTION86.64
4.13-4.720.2311500.16575019X-RAY DIFFRACTION95.69
4.72-5.950.26771520.19015011X-RAY DIFFRACTION95.77
5.95-37.450.24431410.21674752X-RAY DIFFRACTION90.9

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