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- PDB-1bhp: STRUCTURE OF BETA-PUROTHIONIN AT ROOM TEMPERATURE AND 1.7 ANGSTRO... -

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Basic information

Entry
Database: PDB / ID: 1bhp
TitleSTRUCTURE OF BETA-PUROTHIONIN AT ROOM TEMPERATURE AND 1.7 ANGSTROMS RESOLUTION
ComponentsBETA-PUROTHIONIN
KeywordsPLANT TOXIN / THIONINS
Function / homology
Function and homology information


defense response / toxin activity / extracellular region
Similarity search - Function
Thionin-like / Thionin / Thionin-like superfamily / Plant thionin / Plant thionins signature. / Crambin / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Purothionin A-1
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsTeeter, M.M. / Stec, B. / Rao, U.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 2: structure of beta-purothionin at 1.7 A resolution.
Authors: Stec, B. / Rao, U. / Teeter, M.M.
History
DepositionMar 15, 1995-
Revision 1.0Mar 15, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA-PUROTHIONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,3346
Polymers4,9371
Non-polymers3975
Water1,38777
1
A: BETA-PUROTHIONIN
hetero molecules

A: BETA-PUROTHIONIN
hetero molecules

A: BETA-PUROTHIONIN
hetero molecules

A: BETA-PUROTHIONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,33724
Polymers19,7484
Non-polymers1,58920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)53.940, 53.940, 72.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-50-

PO4

21A-52-

ACT

31A-52-

ACT

41A-67-

HOH

51A-90-

HOH

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Components

#1: Protein/peptide BETA-PUROTHIONIN


Mass: 4936.940 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Tissue: GRAIN / References: UniProt: P01543
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal grow
*PLUS
pH: 5.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlbeta-purothionin1drop
22 %dioxane1drop
35 %MPD1drop
458 %ammonium sulfate1drop
575 mMsodium cacodylate1drop
610 %MPD1reservoir
720 %1reservoirMgCl2
890 mMsodium cacodylate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 5160 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.096
Reflection
*PLUS
Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
SDMSSOFTWAREdata collection
PROLSQrefinement
SDMSdata reduction
RefinementResolution: 1.7→10 Å / σ(F): 2.5
RfactorNum. reflection% reflection
Rfree0.281 --
obs0.198 4966 73.2 %
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms337 0 25 77 439
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0310.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.452
X-RAY DIFFRACTIONp_mcangle_it1.772.5
X-RAY DIFFRACTIONp_scbond_it1.563
X-RAY DIFFRACTIONp_scangle_it2.043
X-RAY DIFFRACTIONp_plane_restr0.0080.015
X-RAY DIFFRACTIONp_chiral_restr0.1740.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.5
X-RAY DIFFRACTIONp_multtor_nbd0.190.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.210.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor25
X-RAY DIFFRACTIONp_staggered_tor19.618
X-RAY DIFFRACTIONp_orthonormal_tor1.820
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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