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- PDB-1hyp: CRYSTAL STRUCTURE OF HYDROPHOBIC PROTEIN FROM SOYBEAN; A MEMBER O... -

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Basic information

Entry
Database: PDB / ID: 1hyp
TitleCRYSTAL STRUCTURE OF HYDROPHOBIC PROTEIN FROM SOYBEAN; A MEMBER OF A NEW CYSTINE-RICH FAMILY
ComponentsHYDROPHOBIC PROTEIN FROM SOYBEAN
KeywordsHYDROPHOBIC SEED PROTEIN
Function / homologyHydrophobic seed protein domain / : / Hydrophobic seed protein / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha / Hydrophobic seed protein
Function and homology information
Biological speciesGlycine max (soybean)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsLehmann, M.S.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Crystal structure of hydrophobic protein from soybean; a member of a new cysteine-rich family.
Authors: Baud, F. / Pebay-Peyroula, E. / Cohen-Addad, C. / Odani, S. / Lehmann, M.S.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Data for Soybean Hydrophobic Protein
Authors: Lehmann, M.S. / Pebay-Peyroula, E. / Cohen-Addad, C. / Odani, S.
History
DepositionFeb 5, 1993Processing site: BNL
Revision 1.0Apr 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_residues ...pdbx_database_status / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 4, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROPHOBIC PROTEIN FROM SOYBEAN


Theoretical massNumber of molelcules
Total (without water)8,3641
Polymers8,3641
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.100, 43.300, 28.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HYDROPHOBIC PROTEIN FROM SOYBEAN


Mass: 8363.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycine max (soybean) / References: UniProt: P24337
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.19 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.25 Mammonium sulfate1reservoir
22 M1reservoirNaCl
41.25 Macetic acid1drop
530 mg/mlprotein1drop
60.1 %(v/v)octyl-beta-glucoside1drop
3dioxane1reservoir0.100ml

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 4943 / % possible obs: 78 % / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / % possible obs: 72 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.187 / Highest resolution: 1.8 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms656 0 0 177 833
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.027
X-RAY DIFFRACTIONx_angle_deg4.2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 4647 / σ(F): 3 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS

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