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- PDB-6taa: STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (T... -

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Basic information

Entry
Database: PDB / ID: 6taa
TitleSTRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD
ComponentsALPHA-AMYLASE
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: 2.1 Å
AuthorsSwift, H.J. / Brady, L. / Derewenda, Z.S. / Dodson, E.J. / Turkenburg, J.P. / Wilkinson, A.J.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1991
Title: Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
Authors: Swift, H.J. / Brady, L. / Derewenda, Z.S. / Dodson, E.J. / Dodson, G.G. / Turkenburg, J.P. / Wilkinson, A.J.
#1: Journal: Biochemistry / Year: 1990
Title: Calcium Binding in Alpha-Amylases: An X-Ray Diffraction Study at 2.1 Angstroms Resolution of Two Enzymes from Aspergillus
Authors: Boel, E. / Brady, L. / Brzozowski, A.M. / Derewenda, Z. / Dodson, G.G. / Jensen, V.J. / Petersen, S.B. / Swift, H. / Thim, L. / Woldike, H.F.
History
DepositionAug 21, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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_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
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: ALPHA-AMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6063
Polymers52,5261
Non-polymers802
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.040, 67.183, 133.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 139 AND 341 ARE CIS PROLINES.

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Components

#1: Protein ALPHA-AMYLASE


Mass: 52525.973 Da / Num. of mol.: 1
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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
250 mMsodium acetate1drop
32 mM1dropCaCl2
48 %(w/v)PEG80001drop
516 %PEG80001resrvoir
650 mMsodium acetate1reservoir
72 mM1reservoirCaCl2

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 23794 / Rmerge(I) obs: 0.048 / Num. measured all: 66210

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→7.7 Å / σ(F): 0
Details: SIDE CHAINS OF RESIDUES ALA 1, ASP 5, AND LYS 36 ARE NOT CLEARLY VISIBLE IN ELECTRON DENSITY MAPS, AND ATOMS HAVE BEEN INCLUDED WITH OCCUPANCY ZERO, GIVING RISE TO NON-IDEAL INTERMOLECULAR ...Details: SIDE CHAINS OF RESIDUES ALA 1, ASP 5, AND LYS 36 ARE NOT CLEARLY VISIBLE IN ELECTRON DENSITY MAPS, AND ATOMS HAVE BEEN INCLUDED WITH OCCUPANCY ZERO, GIVING RISE TO NON-IDEAL INTERMOLECULAR DISTANCES AFTER REFINEMENT.
RfactorNum. reflection
obs0.198 23482
Refinement stepCycle: LAST / Resolution: 2.1→7.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 2 239 3927
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0630.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.080.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0091
X-RAY DIFFRACTIONp_mcangle_it1.6021.5
X-RAY DIFFRACTIONp_scbond_it1.9431.5
X-RAY DIFFRACTIONp_scangle_it2.7032
X-RAY DIFFRACTIONp_plane_restr0.020.02
X-RAY DIFFRACTIONp_chiral_restr0.1610.12
X-RAY DIFFRACTIONp_singtor_nbd0.220.5
X-RAY DIFFRACTIONp_multtor_nbd0.2680.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.250.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.91220
X-RAY DIFFRACTIONp_staggered_tor22.90920
X-RAY DIFFRACTIONp_orthonormal_tor35.7520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 7.7 Å / Num. reflection all: 23482 / σ(F): 0 / Rfactor all: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS

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