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- PDB-1od5: Crystal structure of glycinin A3B4 subunit homohexamer -

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Basic information

Entry
Database: PDB / ID: 1od5
TitleCrystal structure of glycinin A3B4 subunit homohexamer
ComponentsGLYCININ
KeywordsGLOBULIN / GLYCININ / SOYBEAN / 11S / SEED STORAGE PROTEIN
Function / homology
Function and homology information


aleurone grain / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CARBONATE ION / Glycinin G5 / Glycinin
Similarity search - Component
Biological speciesGLYCINE MAX (soybean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAdachi, M. / Kanamori, J. / Masuda, T. / Yagasaki, K. / Kitamura, K. / Mikami, B. / Utsumi, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal Structure of Soybean 11S Globulin: Glycinin A3B4 Homohexamer
Authors: Adachi, M. / Kanamori, J. / Masuda, T. / Yagasaki, K. / Kitamura, K. / Mikami, B. / Utsumi, S.
History
DepositionFeb 13, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2003Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 285 TEXT TO EXPLAIN UNUSUAL UNIT-CELL DATA: HEXAGONAL OBVERSE SETTING

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLYCININ
B: GLYCININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,3826
Polymers111,2142
Non-polymers1694
Water3,855214
1
A: GLYCININ
B: GLYCININ
hetero molecules

A: GLYCININ
B: GLYCININ
hetero molecules

A: GLYCININ
B: GLYCININ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,14718
Polymers333,6416
Non-polymers50612
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)114.842, 114.842, 191.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein GLYCININ / GY5


Mass: 55606.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GLYCINE MAX (soybean) / Organ: SEED / References: UniProt: Q39922, UniProt: P04347*PLUS
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHESE ARE SEED STORAGE PROTEINS THAT EXIST AS HEXAMERIC ASSEMBLIES. EACH SUBUNIT IS COMPOSED OF AN ...THESE ARE SEED STORAGE PROTEINS THAT EXIST AS HEXAMERIC ASSEMBLIES. EACH SUBUNIT IS COMPOSED OF AN ACIDIC AND A BASIC CHAIN DERIVED FROM A SINGLE PRECURSOR THAT IS LINKED BY A DISULFIDE BOND.MEMBER OF THE 11S FAMILY OF GLOBULINS.
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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growpH: 5.4 / Details: pH 5.40
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
2MES12pH4.0
3MPD12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→44.3 Å / Num. obs: 55186 / % possible obs: 100 % / Redundancy: 4.13 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 0.08
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.28 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.92 / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 227710 / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 5597 / Num. measured obs: 12780

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Processing

Software
NameClassification
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FXZ

1fxz


Resolution: 2.1→10 Å / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 -10 %RANDOM
Rwork0.201 ---
obs0.201 48190 87.3 %-
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5996 0 10 214 6220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.175 Å / Rfactor Rfree: 0.356 / Rfactor Rwork: 0.301
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19XC.PROTOPHO19X.PRO
X-RAY DIFFRACTION2PARAM.ADACHITOPHO11.PEP
X-RAY DIFFRACTION3TOPHO.ADACHI
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 10 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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