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

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Basic information

Entry
Database: PDB / ID: 1ipj
TitleCRYSTAL STRUCTURES OF RECOMBINANT AND NATIVE SOYBEAN BETA-CONGLYCININ BETA HOMOTRIMERS COMPLEXES WITH N-ACETYL-D-GLUCOSAMINE
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: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,5606
Polymers143,8963
Non-polymers6643
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15710 Å2
ΔGint-74 kcal/mol
Surface area40930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.78, 69.47, 125.33
Angle α, β, γ (deg.)90, 97.22, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BETA-CONGLYCININ, BETA CHAIN


Mass: 47965.461 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Glycine max (soybean) / Organ: SEED / References: UniProt: P25974
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: PEG6000, citrate buffer, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMMES1droppH5.5
30.4 M1dropNaCl
41 mMEDTA1drop
51 mMPMSF1drop
60.02 %1dropNaN3
70.4 M1reservoirNaCl
81 mMEDTA1reservoir
91 mMPMSF1reservoir
100.02 %1reservoirNaN3
117 %PEG100001reservoir
12100 mMMES1reservoirpH5.5

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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: Jul 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. all: 33726 / Num. obs: 72174 / % possible obs: 94.37 % / Redundancy: 2.14 % / Rsym value: 0.055
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 33726 / Num. measured all: 72174 / Rmerge(I) obs: 0.051

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Processing

Software
NameVersionClassification
FRAMBOdata collection
SAINTdata reduction
X-PLORmodel building
X-PLOR3.851refinement
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→7 Å / σ(F): 2 / σ(I): 0
RfactorNum. reflectionSelection details
Rfree0.284 -RANDOM
Rwork0.202 --
obs-20997 -
Refinement stepCycle: LAST / Resolution: 2.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8839 0 42 0 8881
Refinement
*PLUS
Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.217

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