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- PDB-1bag: ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE -

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Basic information

Entry
Database: PDB / ID: 1bag
TitleALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE
ComponentsALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
KeywordsALPHA-AMYLASE / BACILLUS SUBTILIS / MALTOPENTAOSE / CATALYTIC-SITE MUTANT
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding
Similarity search - Function
Starch-binding module 26 / Starch-binding module 26 / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain ...Starch-binding module 26 / Starch-binding module 26 / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta 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 fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsFujimoto, Z. / Mizuno, H. / Takase, K. / Doui, N.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.
Authors: Fujimoto, Z. / Takase, K. / Doui, N. / Momma, M. / Matsumoto, T. / Mizuno, H.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Studies of Wild Type and Catalytic-Site Mutant Alpha-Amylase from Bacillus Subtilis
Authors: Mizuno, H. / Morimoto, Y. / Tsukihara, T. / Matsumoto, T. / Takase, K.
#2: Journal: Biochim.Biophys.Acta / Year: 1992
Title: Site-Directed Mutagenesis of Active Site Residues in Bacillus Subtilis Alpha-Amylase
Authors: Takase, K. / Matsumoto, T. / Mizuno, H. / Yamane, K.
#3: Journal: J.Biochem.(Tokyo) / Year: 1984
Title: Changes in the Properties and Molecular Weights of Bacillus Subtilis M-Type and N-Type Alpha-Amylases Resulting from a Spontaneous Deletion
Authors: Yamane, K. / Hirata, Y. / Furusato, T. / Yamazaki, H. / Nakayama, A.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _struct_site_gen.label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0165
Polymers47,0671
Non-polymers9494
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.590, 74.060, 117.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE / ALPHA-AMYLASE


Mass: 47067.309 Da / Num. of mol.: 1 / Mutation: E208Q
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH MALTOPENTAOSE / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: AMY / Plasmid: PTUB111 / Gene (production host): AMY / Production host: Bacillus subtilis (bacteria) / Strain (production host): 207-25 / References: UniProt: P00691, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2-2-2/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 4

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 10% PEG 3350, 3.5 MM CALCIUM CHLORIDE, 10 MM TRIS/HCL, PH 7.5.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116.4 mg/mlprotein1drop
210 mMTris-HCl1drop
33.5 mM1dropCaCl2
42 %acarbose1drop
50.09-1.23 %G51drop
610 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: COLLIMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 19373 / % possible obs: 80.4 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 5 / % possible all: 44
Reflection
*PLUS
Num. obs: 18097 / Num. measured all: 56354 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.5→7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1676 9.8 %RANDOM
Rwork0.198 ---
obs0.198 17162 80.4 %-
Displacement parametersBiso mean: 15.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-6 Å
Luzzati sigma a0.51 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 59 146 3527
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.241.5
X-RAY DIFFRACTIONx_mcangle_it3.422
X-RAY DIFFRACTIONx_scbond_it3.442
X-RAY DIFFRACTIONx_scangle_it4.82.5
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 174 10 %
Rwork0.268 1563 -
obs--49.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM19X.IONTOPH19X.ION
X-RAY DIFFRACTION4PARAM19.SOLTOPH19X.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21

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