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- PDB-1ua7: Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtili... -

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Entry
Database: PDB / ID: 1ua7
TitleCrystal Structure Analysis of Alpha-Amylase from Bacillus Subtilis complexed with Acarbose
ComponentsAlpha-amylase
KeywordsHYDROLASE / BETA-ALPHA-BARRELS / ACARBOSE / GREEK-KEY MOTIF
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / extracellular region / 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
Chem-ACI / Alpha-amylase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.21 Å
AuthorsKagawa, M. / Fujimoto, Z. / Momma, M. / Takase, K. / Mizuno, H.
Citation
Journal: J.BACTERIOL. / Year: 2003
Title: Crystal structure of Bacillus subtilis alpha-amylase in complex with acarbose
Authors: Kagawa, M. / Fujimoto, Z. / Momma, M. / Takase, K. / Mizuno, H.
#1: 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.
#2: 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.
#3: 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.
#4: 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
DepositionMar 3, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Oct 25, 2017Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.pdbx_synonyms / _struct_conn.ptnr2_label_atom_id
Revision 3.0Jul 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_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_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.pdbx_value_order / _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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Nov 10, 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 3.2Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)47,9048
Polymers46,7971
Non-polymers1,1077
Water7,873437
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.320, 74.204, 115.724
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-amylase / ALPHA-1 / 4-GLUCAN-4-GLUCANOHYDROLASE


Mass: 46796.984 Da / Num. of mol.: 1 / Fragment: residues 4-425 / Mutation: N356Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pNQ356 / Production host: Bacillus subtilis (bacteria) / Strain (production host): 207-25 / References: UniProt: P00691, alpha-amylase

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 310.298 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a21d2m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-quinovopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 442 molecules

#4: Chemical ChemComp-ACI / 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL


Mass: 175.182 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H13NO4 / Comment: antibiotic*YM
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.83 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG 3350, calcium chloride, Tris-HCl, acarbose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→45.49 Å / Num. all: 31194 / Num. obs: 31194 / % possible obs: 93.7 % / Redundancy: 3.46 % / Biso Wilson estimate: 6.5 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 22.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3057 / % possible all: 93.7

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.21→19.97 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2974 10 %RANDOM
Rwork0.208 ---
obs0.208 29744 95.5 %-
all-29744 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5617 Å2 / ksol: 0.346066 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.47 Å20 Å20 Å2
2---4.11 Å20 Å2
3----6.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.21→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 68 437 3808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 440 9.9 %
Rwork0.283 3991 -
obs--85.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4XDICT_22141MOD.PARAM

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