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- PDB-1ud1: Crystal structure of proglycinin mutant C88S -

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Basic information

Entry
Database: PDB / ID: 1ud1
TitleCrystal structure of proglycinin mutant C88S
ComponentsGlycinin G1
KeywordsPLANT PROTEIN / glycinin / soybean / trimer
Function / homology
Function and homology information


protein storage vacuole / nutrient reservoir activity / endoplasmic reticulum
Similarity search - Function
11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold ...11-S seed storage protein, conserved site / 11-S plant seed storage proteins signature. / 11-S seed storage protein, plant / : / Cupin / Cupin 1 / Cupin / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsUtsumi, S. / Adachi, M.
CitationJournal: J.Agric.Food Chem. / Year: 2003
Title: Crystal Structures and Structural Stabilities of the Disulfide Bond-Deficient Soybean Proglycinin Mutants C12G and C88S.
Authors: Adachi, M. / Okuda, E. / Kaneda, Y. / Hashimoto, A. / Shutov, A.D. / Becker, C. / Utsumi, S.
History
DepositionApr 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycinin G1
B: Glycinin G1
C: Glycinin G1


Theoretical massNumber of molelcules
Total (without water)160,9993
Polymers160,9993
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15930 Å2
ΔGint-99 kcal/mol
Surface area36550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.34, 114.34, 145.796
Angle α, β, γ (deg.)90, 90, 90
Int Tables number76
Space group name H-MP41
DetailsThe biological assembly is trimer corresponding to the asymmetric unit.

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Components

#1: Protein Glycinin G1 / proglycinin


Mass: 53666.434 Da / Num. of mol.: 3 / Mutation: C88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04776
Has protein modificationY

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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: 3.94 Å3/Da / Density % sol: 68.5 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG6000, sodium cloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Temperature: 281 K / Method: vapor diffusion, hanging drop / Details: Adachi, M., (2001) J.Mol.Biol., 305, 291.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
28 %PEG60001reservoir
30.1 MMES1reservoir
40.4 M1reservoirNaCl

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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: Aug 25, 1998
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.1→28.9 Å / Num. all: 28221 / Num. obs: 28221 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rsym value: 0.12 / Net I/σ(I): 9.15
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.28 / Rsym value: 0.388 / % possible all: 100
Reflection
*PLUS
Num. obs: 34980 / Rmerge(I) obs: 0.12
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.388

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Processing

Software
NameClassification
SADIEdata collection
SAINTdata reduction
X-PLORmodel building
X-PLORrefinement
SADIEdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.253 2696 RANDOM
Rwork0.193 --
all0.224 26670 -
obs0.224 26670 -
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8649 0 0 0 8649
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg3
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 3.1 Å / Lowest resolution: 3.2 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.226

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