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- PDB-1ipk: CRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYC... -

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Basic information

Entry
Database: PDB / ID: 1ipk
TitleCRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYCININ BETA HOMOTRIMERS
ComponentsBETA-CONGLYCININ, BETA CHAIN
KeywordsSUGAR BINDING PROTEIN / soybean / storage protein / vicilin
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMaruyama, N. / Adachi, M. / Takahashi, K. / Yagasaki, K. / Kohno, M. / Takenaka, Y. / Okuda, E. / Nakagawa, S. / Mikami, B. / Utsumi, S.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Crystal structures of recombinant and native soybean beta-conglycinin beta homotrimers.
Authors: Maruyama, N. / Adachi, M. / Takahashi, K. / Yagasaki, K. / Kohno, M. / Takenaka, Y. / Okuda, E. / Nakagawa, S. / Mikami, B. / Utsumi, S.
History
DepositionMay 16, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CONGLYCININ, BETA CHAIN
B: BETA-CONGLYCININ, BETA CHAIN
C: BETA-CONGLYCININ, BETA CHAIN


Theoretical massNumber of molelcules
Total (without water)144,1003
Polymers144,1003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14950 Å2
ΔGint-87 kcal/mol
Surface area40810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.51, 63.48, 131.43
Angle α, β, γ (deg.)90, 90.01, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-CONGLYCININ, BETA CHAIN


Mass: 48033.496 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25974

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG10000, MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
250 mMcitrate1droppH4.8
30.4 M1dropNaCl
41 mMEDTA1drop
50.1 mMp-APMSF1drop
60.02 %1dropNaN3
75 %PEG60001reservoir
850 mMcitrate1reservoirpH4.8
90.4 M1reservoirNaCl
101 mMEDTA1reservoir
110.1 mMp-APMSF1reservoir
120.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Oct 28, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. all: 101661 / Num. obs: 33007 / % possible obs: 91.02 % / Redundancy: 3.08 % / Rsym value: 0.055
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 101661 / Rmerge(I) obs: 0.055

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Processing

Software
NameClassification
FRAMBOdata collection
SAINTdata reduction
SAINTdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→7 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.275 -RANDOM
Rwork0.205 --
obs-27452 -
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9074 0 0 0 9074
Refinement
*PLUS
Highest resolution: 2.8 Å / Rfactor obs: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.005
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.271

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