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- PDB-2aaa: CALCIUM BINDING IN ALPHA-AMYLASES: AN X-RAY DIFFRACTION STUDY AT ... -

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Entry
Database: PDB / ID: 2aaa
TitleCALCIUM BINDING IN ALPHA-AMYLASES: AN X-RAY DIFFRACTION STUDY AT 2.1 ANGSTROMS RESOLUTION OF TWO ENZYMES FROM ASPERGILLUS
Componentsalpha-amylase
KeywordsGLYCOSIDASE
Function / homology
Function and homology information


alpha-amylase / 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, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Glycoside hydrolase superfamily ...Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / 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
DI(HYDROXYETHYL)ETHER / alpha-amylase / Acid alpha-amylase
Similarity search - Component
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.119 Å
AuthorsBrady, L. / Brzozowski, A.M. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Tsianakas, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 1990
Title: Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A 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
DepositionFeb 27, 1991Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Other
Revision 1.4Jun 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 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Mar 18, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / audit_author / cell / chem_comp / chem_comp_atom / chem_comp_bond / diffrn / diffrn_detector / diffrn_radiation / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / exptl_crystal_grow / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_contact_author / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.angle_alpha / _cell.angle_beta ..._cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_c / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_method_to_determine_struct / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _struct.pdbx_CASP_flag / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Sequence discrepancy
Details: The model was rebuilt and refined in 2025 for which K. Tsianakas was added as a depositor.
Provider: author / Type: Coordinate replacement

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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)54,63210
Polymers52,2281
Non-polymers2,4039
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.1, 98.3, 138
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Atom site foot note1: RESIDUES PRO 139 AND PRO 341 ARE CIS PROLINES.
Components on special symmetry positions
IDModelComponents
11A-879-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein alpha-amylase / 1 / 4-alpha-D-glucan glucanohydrolase


Mass: 52228.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus niger (mold) / Production host: Aspergillus oryzae (mold)
References: UniProt: F1C3F8, UniProt: P56271*PLUS, alpha-amylase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: isolated from a natural source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 289 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.6 Å3/Da / Density % sol: 52.61 %
Crystal growMethod: batch mode / Details: PEG 8000, PH 3.0-4.0 / PH range: 3.0-4.0
Crystal grow
*PLUS
Method: unknown / PH range low: 4 / PH range high: 3
Components of the solutions
*PLUS
Common name: PEG8000

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Data collection

DiffractionSerial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2
DetectorType: SIEMENS-XENTRONICS / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.1 Å
Reflection
*PLUS
Highest resolution: 2.1 Å / Rmerge(I) obs: 0.195

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Processing

Software
NameVersionClassification
Servalcat0.4.105refinement
PDB-REDO8.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.119→69 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rwork0.1116 29290 --
Rfree-1650 -Random selection
obs-30940 97.62 %-
Displacement parametersBiso mean: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.929429118 Å20 Å20 Å2
2---0.375499689 Å20 Å2
3----0.55392943 Å2
Refinement stepCycle: LAST / Resolution: 2.119→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 157 284 4120
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONs_bond_nonh_d0.011739710.012
X-RAY DIFFRACTIONs_angle_nonh_deg1.931854261.7765
X-RAY DIFFRACTIONs_dihedral_angle_1_deg6.64114815
X-RAY DIFFRACTIONs_dihedral_angle_2_deg3.3146885
X-RAY DIFFRACTIONs_dihedral_angle_3_deg10.064889810
X-RAY DIFFRACTIONs_dihedral_angle_6_deg14.969224310
X-RAY DIFFRACTIONs_chiral_restr0.08456250.1282
X-RAY DIFFRACTIONs_planes0.009754900.02
X-RAY DIFFRACTIONs_nbd0.205746670.2
X-RAY DIFFRACTIONs_nbtor0.228462330.2
X-RAY DIFFRACTIONs_hbond_nbd0.12132040.2
X-RAY DIFFRACTIONs_symmetry_nbd0.1838500.2
X-RAY DIFFRACTIONs_symmetry_hbond_nbd0.1977220.2
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkCor.coef. Fo:FcCor.coef. Fo:Fc freeNum. reflection obs% reflection obs (%)
2.119-2.2220.17042060.120733950.9560.9218360187
2.222-2.3420.14131880.102337400.96910.9449392898.72
2.342-2.4840.15811890.103135240.96960.9308371399.23
2.484-2.6550.17012000.10633290.96720.932352999.27
2.655-2.8680.14451740.108230960.96590.9425327099.39
2.868-3.1410.14311650.114428670.96170.9466303299.57
3.141-3.5110.13931340.118326280.96660.9527276299.5
3.511-4.0520.12711300.107623140.97290.9637244499.55
4.052-4.9590.1061210.092919650.97650.9687208699.76
4.959-6.9950.14421010.12715470.9640.9513164899.7
6.995-690.1793420.15748850.9280.924192795.67
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 7 Å / Rfactor obs: 0.169
Solvent computation
*PLUS
Displacement parameters
*PLUS

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