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- PDB-1phs: THE THREE-DIMENSIONAL STRUCTURE OF THE SEED STORAGE PROTEIN PHASE... -

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Basic information

Entry
Database: PDB / ID: 1phs
TitleTHE THREE-DIMENSIONAL STRUCTURE OF THE SEED STORAGE PROTEIN PHASEOLIN AT 3 ANGSTROMS RESOLUTION
ComponentsPHASEOLIN, BETA-TYPE PRECURSOR
KeywordsPLANT SEED STORAGE PROTEIN (VICILIN)
Function / homologyaleurone grain / Cupin / Cupin 1 / Cupin / nutrient reservoir activity / vacuole / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Phaseolin, beta-type
Function and homology information
Biological speciesPhaseolus vulgaris (French bean)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsLawrence, M.C. / Suzuki, E. / Varghese, J.N. / Davis, P.C. / Vandonkelaar, A. / Tulloch, P.A. / Colman, P.M.
Citation
Journal: EMBO J. / Year: 1990
Title: The three-dimensional structure of the seed storage protein phaseolin at 3 A resolution.
Authors: Lawrence, M.C. / Suzuki, E. / Varghese, J.N. / Davis, P.C. / Van Donkelaar, A. / Tulloch, P.A. / Colman, P.M.
#1: Journal: J.Biol.Chem. / Year: 1983
Title: Crystallization of Phaseolin from Phaseolus Vulgaris
Authors: Suzuki, E. / Vandonkelaar, A. / Varghese, J.N. / Lilley, G.G. / Blagrove, R.J. / Colman, P.M.
History
DepositionMar 21, 1990Processing site: BNL
Revision 1.0Oct 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 27, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp_atom / chem_comp_bond / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_ncs_oper
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3]
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHASEOLIN, BETA-TYPE PRECURSOR


Theoretical massNumber of molelcules
Total (without water)45,0431
Polymers45,0431
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PHASEOLIN, BETA-TYPE PRECURSOR

A: PHASEOLIN, BETA-TYPE PRECURSOR

A: PHASEOLIN, BETA-TYPE PRECURSOR


Theoretical massNumber of molelcules
Total (without water)135,1293
Polymers135,1293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation2
Unit cell
Length a, b, c (Å)126.800, 134.500, 161.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1generate(0.24015326, -0.06154476, -0.96881513), (0.93849889, -0.24008369, 0.24775035), (-0.24786933, -0.96886263, -6.958E-5)90.99927, 14.00179, 120.80507
2generate(0.2400531, 0.9386447, -0.24784473), (-0.06134421, -0.24015614, -0.96873014), (-0.96878616, 0.24793041, 0.00010304)-5.04645, 125.97244, 84.67497
3generate(-0.87714645, 0.48033542, 1.902E-5), (0.48011021, 0.87714638, 7.464E-5), (-3.233E-5, -0.00012611, -0.99999993)86.70777, -22.18006, 79.87325
4generate(0.24014024, -0.06135506, 0.96879658), (0.9384829, -0.24020944, -0.24782438), (0.24774304, 0.96889445, 6.92E-5)13.61587, 33.80023, -40.93646
5generate(-0.2400464, -0.93867917, -0.24791947), (0.06137141, 0.24001921, -0.96871144), (0.96878642, -0.24793096, 2.72E-5)151.64488, 85.89973, -4.81743

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Components

#1: Protein PHASEOLIN, BETA-TYPE PRECURSOR / Coordinate model: Cα atoms only


Mass: 45043.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaseolus vulgaris (French bean) / References: UniProt: P02853

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion
Details: taken from Suzuki, E. et al (1983). J. Biol. Chem., 258, 2634-2636.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 %satammonium sulfate1drop
370 %satammonium sulfate1reservoiror 23% ethanol

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Data collection

Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 41688 / % possible obs: 74 % / Rmerge(I) obs: 0.102

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3→6 Å /
RfactorNum. reflection
Rwork0.225 -
obs-34024
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms364 0 0 0 364
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.73
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
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / Num. reflection obs: 34024 / Rfactor obs: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.73

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