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- PDB-2taa: STRUCTURE AND POSSIBLE CATALYTIC RESIDUES OF TAKA-AMYLASE A -

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Basic information

Entry
Database: PDB / ID: 2taa
TitleSTRUCTURE AND POSSIBLE CATALYTIC RESIDUES OF TAKA-AMYLASE A
ComponentsTAKA-AMYLASE A
KeywordsHYDROLASE (O-GLYCOSYL)
Function / homology
Function and homology information


cell wall-bounded periplasmic space / hyphal septin band / spitzenkorper / fungal-type cell wall / alpha-amylase / cell septum / alpha-amylase activity / carbohydrate catabolic process / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases ...Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / 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 A type-1/2 / Alpha-amylase A type-3
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsKusunoki, M. / Matsuura, Y. / Tanaka, N. / Kakudo, M.
Citation
Journal: J.Biochem.(Tokyo) / Year: 1984
Title: Structure and possible catalytic residues of Taka-amylase A
Authors: Matsuura, Y. / Kusunoki, M. / Harada, W. / Kakudo, M.
#1: Journal: J.Biochem.(Tokyo) / Year: 1980
Title: Molecular Structure of Taka-Amylase A. I. Backbone Chain Folding at 3 Angstroms Resolution
Authors: Matsuura, Y. / Kusunoki, M. / Harada, W. / Tanaka, N. / Iga, Y. / Yasuoka, N. / Toda, H. / Narita, K. / Kakudo, M.
#2: Journal: J.Biochem.(Tokyo) / Year: 1979
Title: Low Resolution Crystal Structures of Taka-Amylase a and its Complexes with Inhibitors
Authors: Matsuura, Y. / Kusunoki, M. / Date, W. / Harada, S. / Bando, S. / Tanaka, N. / Kakudo, M.
History
DepositionOct 18, 1982Processing site: BNL
SupersessionOct 21, 1982ID: 1TAA
Revision 1.0Oct 21, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jun 5, 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_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_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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700SHEET THE NINE-STRANDED SHEET BS1 DESCRIBED BELOW IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS ...SHEET THE NINE-STRANDED SHEET BS1 DESCRIBED BELOW IS ACTUALLY AN EIGHT-STRANDED BETA BARREL. THIS IS DENOTED BY THE FIRST STRAND RECURRING AS THE LAST STRAND.
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAKA-AMYLASE A
B: TAKA-AMYLASE A
C: TAKA-AMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,4316
Polymers157,3103
Non-polymers1203
Water00
1
A: TAKA-AMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4772
Polymers52,4371
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TAKA-AMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4772
Polymers52,4371
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TAKA-AMYLASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4772
Polymers52,4371
Non-polymers401
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.900, 133.300, 94.300
Angle α, β, γ (deg.)90.00, 102.70, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES 475 THROUGH 478 ARE POORLY DEFINED IN THE ELECTRON DENSITY MAP.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.537662, 0.842761, 0.003491), (-0.843195, -0.537874, -0.015704), (-0.011223, -0.011613, 0.999697)-13.11357, 15.05393, 37.58095
2given(0.494189, 0.868623, 0.024926), (0.869382, -0.494682, 0.002191), (0.014088, 0.020356, -0.999516)-18.69613, 40.90763, 4.56432
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT FOR THIS ENTRY CONTAINS THREE AMYLASE MOLECULES. THEY CAN BE GENERATED FROM CHAIN A OF THIS ENTRY BY APPLYING THE NON-CRYSTALLOGRAPHIC THREE-FOLD SCREW AXIS GIVEN BY THE MTRIX RECORDS BELOW.

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Components

#1: Protein TAKA-AMYLASE A


Mass: 52436.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold)
References: UniProt: P10529, UniProt: P0C1B3*PLUS, alpha-amylase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal grow
*PLUS
Method: unknown

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementHighest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11070 0 3 0 11073
Refinement
*PLUS
Highest resolution: 3 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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