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- PDB-1amy: CRYSTAL AND MOLECULAR STRUCTURE OF BARLEY ALPHA-AMYLASE -

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Entry
Database: PDB / ID: 1amy
TitleCRYSTAL AND MOLECULAR STRUCTURE OF BARLEY ALPHA-AMYLASE
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
Alpha-amylase type B isozyme
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKadziola, A. / Haser, R.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Crystal and molecular structure of barley alpha-amylase.
Authors: Kadziola, A. / Abe, J. / Svensson, B. / Haser, R.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Characterization, Crystallization and Crystallographic Preliminary Data of the Complex between Barley Alpha-Amylase and the Bifunctional Alpha-Amylase(Slash)Subtilisin Inhibitor from Barley Seeds
Authors: Vallee, F. / Kadziola, A. / Bourne, Y. / Abe, J.-I. / Svensson, B. / Haser, R.
#2: Journal: J.Biol.Chem. / Year: 1993
Title: Site-Directed Mutagenesis of Histidine 93, Aspartic Acid 180, Glutamic Acid 20 5, Histidine 290, and Aspartic Acid 291 at the Active Site and Tryptophan 279 at the Raw Starch Binding Site in Barley Alpha-Amylase 1
Authors: Sogaard, M. / Kadziola, A. / Haser, R. / Svensson, B.
History
DepositionMar 10, 1994Processing site: BNL
Revision 1.0May 13, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _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.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_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_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
Remark 700SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)45,1074
Polymers44,9861
Non-polymers1203
Water2,738152
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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
Atom site foot note1: CIS PROLINE - PRO 129

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Components

#1: Protein 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE


Mass: 44986.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / References: UniProt: P04063, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE CAN BE DESCRIBED AS CONSISTING OF THREE DOMAINS: A CENTRAL DOMAIN (A) FORMING AN ...THE STRUCTURE CAN BE DESCRIBED AS CONSISTING OF THREE DOMAINS: A CENTRAL DOMAIN (A) FORMING AN ALPHA-BETA-8-BARREL (GLN 1 - ILE 88 AND ASN 153 - HIS 344) WITH A PROTRUDING IRREGULARLY STRUCTURED LOOP DOMAIN (B) (VAL 89 - LEU 152) AND A C-TERMINAL DOMAIN (C) (LYS 351 - ILE 403) FORMING AN ANTI-PARALLEL FIVE STRANDED BETA-SHEET. THE ACTIVE CATALYTIC SITE CLEFT (AS) HAS BEEN LOCATED TO THE C-TERMINAL END OF THE CENTRAL BETA-BARREL AROUND RESIDUES ASP 179, GLU 204 AND ASP 289. A RAW STARCH BINDING SITE (SS) HAS BEEN LOCATED AT THE SURFACE AROUND RESIDUES TRP 276 AND TRP 277.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.64 %
Crystal
*PLUS
Density % sol: 75 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein1drop
210 mMMes1drop
310 mM1dropNaOH
45 mM1dropCaCl2
50.4-1.0 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.77 Å / Num. obs: 19542 / % possible obs: 89 % / Num. measured all: 109747 / Rmerge(I) obs: 0.151

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.8→10 Å / σ(F): 1
Details: IN A FINAL 2FOBS-FCALC MAP NO DENSITY WAS SEEN FOR THE SIDE CHAINS OF LYS 158, TYR 378, AND LYS 389.
RfactorNum. reflection
Rwork0.153 -
obs0.153 18303
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 3 152 3339
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg3.3
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.92 Å / Num. reflection obs: 1386 / Rfactor obs: 0.233

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