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- PDB-1wuw: Crystal Structure of beta hordothionin -

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Basic information

Entry
Database: PDB / ID: 1wuw
TitleCrystal Structure of beta hordothionin
ComponentsBeta-hordothionin
KeywordsPLANT PROTEIN / crambin fold / dimer
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
SERINE / PARA-TOLUENE SULFONATE / Beta-hordothionin
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJohnson, K.A. / Kim, E. / Teeter, M.M. / Suh, S.W. / Stec, B.
CitationJournal: Febs Lett. / Year: 2005
Title: Crystal structure of alpha-hordothionin at 1.9 Angstrom resolution.
Authors: Johnson, K.A. / Kim, E. / Teeter, M.M. / Suh, S.W. / Stec, B.
History
DepositionDec 9, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 4, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id ..._refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Beta-hordothionin
B: Beta-hordothionin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4286
Polymers9,8742
Non-polymers5554
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-7 kcal/mol
Surface area5970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.660, 68.660, 47.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-256-

HOH

21A-275-

HOH

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Components

#1: Protein/peptide Beta-hordothionin


Mass: 4936.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / References: UniProt: P21742
#2: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE / P-Toluenesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 2000, citrate, ammonium sulfate, toluene sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: AREA DETECTOR / Date: Jun 21, 1994 / Details: monochromator
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 8963 / Num. obs: 8963 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.1 % / Rmerge(I) obs: 0.078
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 12.2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 8.1 / Num. unique all: 364 / % possible all: 54

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Processing

Software
NameClassification
MADNESSdata collection
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
MADNESSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bhp

1bhp


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 465 -random
Rwork0.172 ---
obs0.172 8963 93 %-
all-8963 --
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms674 0 36 92 802
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.032
LS refinement shellResolution: 1.9→1.95 Å
RfactorNum. reflection% reflection
Rfree0.34 18 -
Rwork0.22 --
obs-364 54 %

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