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- PDB-1ava: AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED -

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Basic information

Entry
Database: PDB / ID: 1ava
TitleAMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED
Components
  • BARLEY ALPHA-AMYLASE 2(CV MENUET)
  • BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
KeywordsHYDROLASE INHIBITION / ENZYME INHIBITOR COMPLEX
Function / homology
Function and homology information


alpha-amylase inhibitor activity / starch catabolic process / alpha-amylase / alpha-amylase activity / serine-type endopeptidase inhibitor activity / calcium ion binding
Similarity search - Function
Alpha-amylase, C-terminal beta-sheet / Alpha-amylase, plant / Alpha-amylase C-terminal beta-sheet domain / Alpha-amylase C-terminal beta-sheet domain / Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Alpha amylase / Kunitz inhibitor STI-like superfamily ...Alpha-amylase, C-terminal beta-sheet / Alpha-amylase, plant / Alpha-amylase C-terminal beta-sheet domain / Alpha-amylase C-terminal beta-sheet domain / Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature. / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Alpha amylase / Kunitz inhibitor STI-like superfamily / Alpha amylase, catalytic domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Alpha-amylase type B isozyme / Alpha-amylase/subtilisin inhibitor
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / PHASE COMBINATION / Resolution: 1.9 Å
AuthorsVallee, F. / Kadziola, A. / Bourne, Y. / Juy, M. / Svensson, B. / Haser, R.
Citation
Journal: Structure / Year: 1998
Title: Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
Authors: Vallee, F. / Kadziola, A. / Bourne, Y. / Juy, M. / Rodenburg, K.W. / Svensson, B. / Haser, R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Characterization, Crystallization and Preliminary X-Ray Crystallographic Analysis of the Complex between Barley Alpha-Amylase and the Bifunctional Alpha-Amylase/Subtilisin Inhibitor from Barley Seeds
Authors: Vallee, F. / Kadziola, A. / Bourne, Y. / Abe, J. / Svensson, B. / Haser, R.
History
DepositionSep 15, 1997Processing site: BNL
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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: BARLEY ALPHA-AMYLASE 2(CV MENUET)
B: BARLEY ALPHA-AMYLASE 2(CV MENUET)
C: BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
D: BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,11012
Polymers129,7904
Non-polymers3218
Water13,475748
1
A: BARLEY ALPHA-AMYLASE 2(CV MENUET)
C: BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0556
Polymers64,8952
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-58 kcal/mol
Surface area21560 Å2
MethodPISA
2
B: BARLEY ALPHA-AMYLASE 2(CV MENUET)
D: BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0556
Polymers64,8952
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-54 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.500, 96.180, 170.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.98826, 0.144042, 0.050931), (-0.152186, 0.898692, 0.41133), (0.013477, -0.414252, 0.910062)
Vector: -24.18795, -0.3904, 1.53174)

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Components

#1: Protein BARLEY ALPHA-AMYLASE 2(CV MENUET) / AMY2


Mass: 44986.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: SEED / References: UniProt: P04063, alpha-amylase
#2: Protein BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR / BASI


Mass: 19908.314 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: SEED / References: UniProt: P07596
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal
*PLUS
Density % sol: 45 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.4 mg/mlprotein1drop
23-8 %PEG60001reservoir
310 mMMES1reservoir
45 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1994
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 95258 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rsym value: 0.105
Reflection shellResolution: 1.9→2.1 Å / % possible all: 82.5
Reflection
*PLUS
Num. obs: 95528
Reflection shell
*PLUS
% possible obs: 82.5 %

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: PHASE COMBINATION
Starting model: AMY2

Resolution: 1.9→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -10 %RANDOM
Rwork0.208 ---
obs0.208 88165 91.3 %-
Displacement parametersBiso mean: 19.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9176 0 8 749 9933
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.45
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.12.2
X-RAY DIFFRACTIONx_mcangle_it22.1
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→2.1 Å / % reflection Rfree: 10 % / % reflection obs: 82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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