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- PDB-1e40: Tris/maltotriose complex of chimaeric amylase from B. amyloliquef... -

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Basic information

Entry
Database: PDB / ID: 1.0E+40
TitleTris/maltotriose complex of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 2.2A
ComponentsALPHA-AMYLASE
KeywordsHYDROLASE / AMYLASE / FAMILY 13 / MALTOTRIOSE / TRIS / COMPLEX
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding / extracellular region
Similarity search - Function
Alpha-amylase, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / 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, thermostable / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / 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-maltotriose / Alpha-amylase / Alpha-amylase
Similarity search - Component
Biological speciesBACILLUS AMYLOLIQUEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J.
CitationJournal: Biochemistry / Year: 2000
Title: Structural Analysis of a Chimeric Bacterial Alpha-Amylase. High Resolution Analysis of Native and Ligand Complexes
Authors: Brzozowski, A.M. / Lawson, D.M. / Turkenburg, J.P. / Bisgaard-Frantzen, H. / Svendsen, A. / Borchert, T.V. / Dauter, Z. / Wilson, K.S. / Davies, G.J.
History
DepositionJun 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp ..._exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_database_status.status_code_sf / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 2.1Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)55,8488
Polymers55,0381
Non-polymers8107
Water9,710539
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)52.720, 78.270, 238.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein ALPHA-AMYLASE /


Mass: 55038.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHIMAERIC STRUCTURE CONSISTING OF RESIDUES 1 - 300 OF B. AMYLOLIQUEFACIENS AND RESIDUES 301 - 483 OF B. LICHENIFORMIS IN COMPLEX WITH TRIS AND MALTOTRIOSE
Source: (gene. exp.) BACILLUS AMYLOLIQUEFACIENS (bacteria) / Description: SYNTHETIC GENE / Production host: BACILLUS AMYLOLIQUEFACIENS (bacteria) / References: UniProt: P00692, UniProt: P06278, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 545 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 539 / 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: 2.34 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING ...Details: CRYSTALS WERE GROWN AT 18C USING THE HANGING DROP METHOD WITH 8-13% MONOMETHYL ETHER POLYETHYLENE GLYCOL 2000 OR 5000 AS PRECIPITANT. DROPS WERE BUFFERED WITH 0.1M TRIS/HCL PH 7.5 CONTAINING 5MM CACL2 AND THE PROTEIN CONCENTRATION WAS 30-35MG/ML. CRYSTALS WERE THEN SOAKED IN 10MM MALTOTRIOSE SOLUTION TO OBTAIN THE COMPLEX.
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
18-13 %(w/v)mmePEG20001reservoiror PEG5000
20.1 MTris-HCl1drop
35 mM1dropCaCl2
430-35 Mprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 15, 1994
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 23662 / % possible obs: 94 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 13 / % possible all: 77
Reflection
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 77 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 13

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E3X

1e3x


Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.3 / ESU R Free: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1141 5 %RANDOM
Rwork0.13 ---
obs-23662 94 %-
Displacement parametersBiso mean: 12.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3900 0 47 539 4486
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0310.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3222
X-RAY DIFFRACTIONp_mcangle_it1.9363
X-RAY DIFFRACTIONp_scbond_it1.7722
X-RAY DIFFRACTIONp_scangle_it2.7323
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1090.15
X-RAY DIFFRACTIONp_singtor_nbd0.1730.3
X-RAY DIFFRACTIONp_multtor_nbd0.1970.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1410.3
X-RAY DIFFRACTIONp_planar_tor3.47
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.820
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.13
Solvent computation
*PLUS
Displacement parameters
*PLUS

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