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- PDB-1wba: WINGED BEAN ALBUMIN 1 -

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Basic information

Entry
Database: PDB / ID: 1wba
TitleWINGED BEAN ALBUMIN 1
ComponentsWINGED BEAN ALBUMIN 1
KeywordsSEED STORAGE PROTEIN / ALBUMIN
Function / homology
Function and homology information


nutrient reservoir activity / endopeptidase inhibitor activity
Similarity search - Function
Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesPsophocarpus tetragonolobus (winged bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR, MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMccoy, A.J.
CitationJournal: J.Biol.Chem. / Year: 1987
Title: Crystallization and preliminary crystallographic data of the major albumin from Psophocarpus tetragonolobus (L.) DC.
Authors: Dayan, S.M. / Van Donkelaar, A. / Kortt, A.A.
History
DepositionJun 19, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_special_symmetry / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WINGED BEAN ALBUMIN 1


Theoretical massNumber of molelcules
Total (without water)19,3571
Polymers19,3571
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.600, 95.600, 86.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-256-

HOH

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Components

#1: Protein WINGED BEAN ALBUMIN 1


Mass: 19356.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Psophocarpus tetragonolobus (winged bean) / References: UniProt: P15465
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion / pH: 5.5
Details: VAPOR DIFFUSION FROM PROTEIN AT 5MG/ML IN 0.1M SUCCINATE BUFFER PH 5.5 EQUILIBRATED AGAINST 30% ETHANOL., vapor diffusion
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 30 % / Common name: ethanol

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Dec 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12039 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 10.1 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 4.2

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Processing

Software
NameClassification
WEISdata collection
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
Agrovatadata scaling
X-PLORphasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: SOYBEAN TRYPSIN INHIBITOR

Resolution: 1.8→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.19 --
obs0.19 15159 80 %
Displacement parametersBiso mean: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1-9.5 Å29.5 Å29.5 Å2
2--9.5 Å29.5 Å2
3---9.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 0 87 1398
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.531
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.87
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.207
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: 1.8→2 Å
RfactorNum. reflection% reflection
Rwork0.221 2156 -
obs--43 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.874
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.207

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