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- PDB-2plh: STRUCTURE OF ALPHA-1-PUROTHIONIN AT ROOM TEMPERATURE AND 2.8 ANGS... -

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Basic information

Entry
Database: PDB / ID: 2plh
TitleSTRUCTURE OF ALPHA-1-PUROTHIONIN AT ROOM TEMPERATURE AND 2.8 ANGSTROMS RESOLUTION
ComponentsALPHA-1-PUROTHIONIN
KeywordsTOXIN / MEMBRANE ACTIVE / DISULFIDE RICH
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 / 2-BUTANOL / Alpha-1-purothionin
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsTeeter, M.M. / Stec, B. / Rao, U.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Refinement of purothionins reveals solute particles important for lattice formation and toxicity. Part 1: alpha1-purothionin revisited.
Authors: Rao, U. / Stec, B. / Teeter, M.M.
#1: Journal: Proteins / Year: 1990
Title: Crystal Structure of a Protein-Toxin Alpha1-Purothionin at 2.5 Angstroms and a Comparison with Predicted Models
Authors: Teeter, M.M. / Ma, X.-Q. / Rao, U. / Whitlow, M.
History
DepositionJul 9, 1993Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1-PUROTHIONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,4409
Polymers4,8361
Non-polymers6058
Water1,946108
1
A: ALPHA-1-PUROTHIONIN
hetero molecules

A: ALPHA-1-PUROTHIONIN
hetero molecules

A: ALPHA-1-PUROTHIONIN
hetero molecules

A: ALPHA-1-PUROTHIONIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,76236
Polymers19,3434
Non-polymers2,41832
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)53.590, 53.590, 69.790
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-85-

ACT

21A-85-

ACT

31A-116-

PO4

41A-123-

ACT

51A-123-

ACT

61A-59-

HOH

71A-78-

HOH

81A-105-

HOH

91A-108-

HOH

101A-117-

HOH

111A-119-

HOH

121A-138-

HOH

131A-142-

HOH

141A-171-

HOH

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Components

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Protein/peptide , 1 types, 1 molecules A

#1: Protein/peptide ALPHA-1-PUROTHIONIN


Mass: 4835.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SOLUTE MOLECULES NOT ADDED TO THE / Source: (natural) Triticum aestivum (bread wheat) / Tissue: GRAIN / References: UniProt: P01544

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-SBT / 2-BUTANOL


Mass: 74.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.5 %
Description: AREA DETECTOR AND DIFFRACTOMETER DATA SETS WERE MERGED
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1180 mg/mlprotein1drop
275 mMsodium cacodylate1drop
315 %(v/v)sec-butanol1drop
48 %(v/v)sec-butanol1reservoir
590 mMsodium cacodylate1reservoir
620 %(v/v)sat1reservoirMgCl2

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: CRAD, P21 / Date: Jan 1, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. obs: 2106 / % possible obs: 61.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.123
Reflection
*PLUS
Rmerge(I) obs: 0.123

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Processing

Software
NameVersionClassification
DTP(MIT)data collection
PROLSQrefinement
DTPdata reduction
RefinementResolution: 2.5→10 Å / σ(F): 2 /
RfactorNum. reflection
obs0.155 1168
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms330 0 39 108 477
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0260.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.532
X-RAY DIFFRACTIONp_mcangle_it0.862.5
X-RAY DIFFRACTIONp_scbond_it0.6033
X-RAY DIFFRACTIONp_scangle_it0.9112
X-RAY DIFFRACTIONp_plane_restr0.0050.015
X-RAY DIFFRACTIONp_chiral_restr0.1120.15
X-RAY DIFFRACTIONp_singtor_nbd0.0950.1
X-RAY DIFFRACTIONp_multtor_nbd0.0740.1
X-RAY DIFFRACTIONp_xhyhbond_nbd0.0790.1
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor13
X-RAY DIFFRACTIONp_staggered_tor18.118
X-RAY DIFFRACTIONp_orthonormal_tor9.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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