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- PDB-1hss: 0.19 ALPHA-AMYLASE INHIBITOR FROM WHEAT -

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Basic information

Entry
Database: PDB / ID: 1hss
Title0.19 ALPHA-AMYLASE INHIBITOR FROM WHEAT
Components0.19 ALPHA-AMYLASE INHIBITOR
KeywordsCEREAL INHIBITOR / ANIMAL AMYLASE
Function / homology
Function and homology information


alpha-amylase inhibitor activity / IgE binding / serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Cereal seed allergen/trypsin and alpha-amylase inhibitor, conserved site / Cereal trypsin/alpha-amylase inhibitors family signature. / Cereal seed allergen/grain softness/trypsin and alpha-amylase inhibitor / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-amylase inhibitor 0.19
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / ISOMORPHOUS REPLACEMENT / Resolution: 2.06 Å
AuthorsOda, Y. / Fukuyama, K.
Citation
Journal: Biochemistry / Year: 1997
Title: Tertiary and quaternary structures of 0.19 alpha-amylase inhibitor from wheat kernel determined by X-ray analysis at 2.06 A resolution.
Authors: Oda, Y. / Matsunaga, T. / Fukuyama, K. / Miyazaki, T. / Morimoto, T.
#1: Journal: J.Biochem.(Tokyo) / Year: 1994
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Alpha-Amylase Inhibitor Coded 0.19 From Wheat Kernel
Authors: Miyazaki, T. / Morimoto, T. / Fukuyama, K. / Matsubara, H.
History
DepositionJul 1, 1997Processing site: BNL
Revision 1.0Jul 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 0.19 ALPHA-AMYLASE INHIBITOR
B: 0.19 ALPHA-AMYLASE INHIBITOR
C: 0.19 ALPHA-AMYLASE INHIBITOR
D: 0.19 ALPHA-AMYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)53,4014
Polymers53,4014
Non-polymers00
Water4,756264
1
A: 0.19 ALPHA-AMYLASE INHIBITOR
B: 0.19 ALPHA-AMYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)26,7012
Polymers26,7012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area10270 Å2
MethodPISA
2
C: 0.19 ALPHA-AMYLASE INHIBITOR
D: 0.19 ALPHA-AMYLASE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)26,7012
Polymers26,7012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.300, 79.300, 60.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999914, 0.012483, 0.004048), (0.001677, -0.184413, 0.982847), (0.013015, 0.98277, 0.184376)-48.2123, 26.94972, -22.07434
2given(-0.992683, -0.043094, 0.112794), (-0.119788, 0.234027, -0.964822), (0.015181, -0.971275, -0.237477)-47.63682, -28.19507, 26.06169
3given(0.992469, 0.121661, -0.014296), (0.12209, -0.991919, 0.034516), (-0.009982, -0.036001, -0.999302)-3.513, 5.2578, 4.33391
DetailsWHEAT KERNEL 0.19 ALPHA-AMYLASE INHIBITOR EXISTS AS A HOMODIMER IN SOLUTION. AN ASYMMETRIC UNIT CONTAINS TWO DIMERS. THREE NON-CRYSTALLOGRAPHIC TWO-FOLD AXES WHICH ARE PERPENDICULAR TO EACH OTHER RELATE THE FOUR MONOMERS. A: FIRST MOLECULE IN AN ASYMMETRIC UNIT. IT FORMS A BIOLOGICAL DIMER WITH CHAIN B. B: SECOND MOLECULE IN AN ASYMMETRIC UNIT. IT FORMS A BIOLOGICAL DIMER WITH CHAIN A. C: THIRD MOLECULE IN AN ASYMMETRIC UNIT. IT FORMS A BIOLOGICAL DIMER WITH CHAIN D. D: FOURTH MOLECULE IN AN ASYMMETRIC UNIT. IT FORMS A BIOLOGICAL DIMER WITH CHAIN C.

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Components

#1: Protein
0.19 ALPHA-AMYLASE INHIBITOR


Mass: 13350.370 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Triticum aestivum (bread wheat) / Organ: KERNEL / References: UniProt: P01085
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD.
Crystal growpH: 7
Details: PROTEIN WAS CRYSTALLIZED FROM 100MM NACL, 20MM HEPES, PH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 R.T. / Method: microdialysis / Details: Miyazaki, T., (1994) J.Biochem.(Tokyo), 115, 179.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMPIPES12
2100 mg/ml12NaCl
310 mg/mlprotein11

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.07 Å / Num. obs: 22687 / % possible obs: 81.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 49815
Reflection shell
*PLUS
% possible obs: 67.3 % / Rmerge(I) obs: 0.15

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Processing

Software
NameVersionClassification
RIGAKUSOFTWAREdata collection
RIGAKUSOFTWAREdata reduction
X-PLORmodel building
X-PLORrefinement
RIGAKUdata scaling
X-PLORphasing
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 2.06→10 Å / Cross valid method: FREE R-VALUE / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -9 %RANDOM
Rwork0.187 ---
obs0.187 22462 --
Displacement parametersBiso mean: 32.8 Å2
Refine analyzeLuzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 2.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3628 0 0 264 3892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL

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