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- PDB-1bg9: BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE -

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Basic information

Entry
Database: PDB / ID: 1bg9
TitleBARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE
Components1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
KeywordsHYDROLASE / O-GLYCOSYL
Function / homology
Function and homology information


starch catabolic process / alpha-amylase / alpha-amylase 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 / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...Alpha-amylase, C-terminal beta-sheet / Alpha-amylase, plant / Alpha-amylase C-terminal beta-sheet domain / Alpha-amylase C-terminal beta-sheet domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / 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
Chem-AF1 / Alpha-amylase type B isozyme
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / REFINEMENT DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsKadziola, A. / Haser, R.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.
Authors: Kadziola, A. / Sogaard, M. / Svensson, B. / Haser, R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal and Molecular Structure of Barley Alpha-Amylase
Authors: Kadziola, A. / Abe, J.I. / Svensson, B. / Haser, R.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.process_site / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9056
Polymers44,9861
Non-polymers9195
Water2,666148
1
A: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
hetero molecules

A: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,81112
Polymers89,9732
Non-polymers1,83810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)135.200, 135.200, 79.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE / ALPHA-AMYLASE / HIGH PI ISOZYME


Mass: 44986.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hordeum vulgare (barley) / Organ: GERMINATED SEEDS / Variant: CULTIVAR MENUET / References: UniProt: P04063, alpha-amylase
#2: Polysaccharide 4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5- ...4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 477.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
[][b-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Sugar ChemComp-AF1 / 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucopyranose / 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucose / 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-D-glucose / 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-glucose


Type: D-saccharide, beta linking / Mass: 321.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C13H23NO8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 4.67 Å3/Da / Density % sol: 75 %
Description: COMPLEX BETWEEN BARLEY ALPHA-AMYLASE AND SUBSTRATE ANALOGUE ACARBOSE
Crystal growpH: 6.7 / Details: pH 6.7
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: Svensson, B., (1987) J. Biol. Chem., 262, 13682.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mM1dropCaCl2
210 mMMES1drop
34-16 mg/mlprotein1drop
410 %satammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Apr 1, 1992
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.729 Å / Num. obs: 17688 / % possible obs: 90.5 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 16.6
Reflection shellResolution: 2.729→2.9 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.27 / % possible all: 44.8
Reflection
*PLUS
Num. measured all: 61039
Reflection shell
*PLUS
% possible obs: 44.8 %

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Processing

Software
NameVersionClassification
X-PLOR2.1model building
X-PLOR2.1refinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
XENGENdata scaling
X-PLOR2.1phasing
RefinementMethod to determine structure: REFINEMENT DIFFERENCE FOURIER
Starting model: 1AMY

1amy


Resolution: 2.8→10 Å
Cross valid method: THE VERSION OF X-PLOR (2.1) ORIGINALLY USED FOR REFINEMENT THE FREE R TEST WAS NOT AN OPTION. THEREFORE WE HAVE GIVEN THE OVERALL R FACTOR (TEST+WORKING) INSTEAD OF (WORK) ...Cross valid method: THE VERSION OF X-PLOR (2.1) ORIGINALLY USED FOR REFINEMENT THE FREE R TEST WAS NOT AN OPTION. THEREFORE WE HAVE GIVEN THE OVERALL R FACTOR (TEST+WORKING) INSTEAD OF (WORK) TOGETHER WITH AN ESTIMATE OF THE FREE R (TEST) VALUE BASED ON A SIMULATED ANNEALING REFINEMENT WITH A NEWER VERSION OF X-PLOR (3.1).
σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1729 10 %RANDOM
Rwork0.151 ---
obs0.151 17688 86.4 %-
Displacement parametersBiso mean: 20.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-10 Å
Luzzati sigma a0.35 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 58 148 3390
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d1.5
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_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.335 141 9.6 %
Rwork0.225 1466 -
obs--60.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2TOP.ACAR
Software
*PLUS
Name: X-PLOR / Version: 2.1,3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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