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- PDB-3bc9: Alpha-amylase B in complex with acarbose -

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Basic information

Entry
Database: PDB / ID: 3bc9
TitleAlpha-amylase B in complex with acarbose
ComponentsAlpha amylase, catalytic region
KeywordsHYDROLASE / alpha-amylase / acarbose / thermostable / halophilic / N domain / raw starch binding
Function / homology
Function and homology information


glucan 1,4-alpha-maltohexaosidase / glucan 1,4-alpha-maltohexaosidase activity / alpha-amylase activity / carbohydrate metabolic process / extracellular space / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / Alpha-amylase C-terminal, prokaryotic / Alpha-amylase C-terminal / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-acarbose / Chem-ACI / alpha-D-glucopyranose / Alpha amylase / :
Similarity search - Component
Biological speciesHalothermothrix orenii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.35 Å
AuthorsTan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structure of the Polyextremophilic alpha-Amylase AmyB from Halothermothrix orenii: Details of a Productive Enzyme-Substrate Complex and an N Domain with a Role in Binding Raw Starch
Authors: Tan, T.-C. / Mijts, B.N. / Swaminathan, K. / Patel, B.K.C. / Divne, C.
History
DepositionNov 12, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Oct 25, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / database_PDB_caveat / diffrn_source
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.pdbx_synonyms / _diffrn_source.pdbx_synchrotron_site
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / entity_name_com / 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_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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_PDB_caveat.text / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha amylase, catalytic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,23014
Polymers68,5811
Non-polymers2,64913
Water10,341574
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)227.850, 77.240, 50.380
Angle α, β, γ (deg.)90.00, 98.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha amylase, catalytic region / amyb


Mass: 68580.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halothermothrix orenii (bacteria) / Strain: H 168 / Gene: amyb / Plasmid: pET-19B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q2ADF2, UniProt: B8CZ54*PLUS, alpha-amylase

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Sugars , 5 types, 6 molecules

#2: Polysaccharide alpha-D-quinovopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 326.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DQuipa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2122m-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(4+1)][a-D-6-deoxy-Glcp]{}}LINUCSPDB-CARE
#3: 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
[][D-1-deoxy-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}LINUCSPDB-CARE
#4: Polysaccharide 4,6-dideoxy-alpha-D-xylo-hexopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 472.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a2122h-1a_1-5][a21d2m-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-4,6-deoxy-Glcp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 645.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-acarbose
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5][a2122m-1a_1-5_4*NC^SC^SC^SC^RCCO/7=^ZC$3/6O/5O/4O]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 581 molecules

#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M sodium acetate, 0.1M Mes-OH, 20% (w/v) PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2007 / Details: toroid mirrors
RadiationMonochromator: Si(111) double crystal monochromator, water-cooled
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 188142 / Num. obs: 188142 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rsym value: 0.076 / Net I/σ(I): 10.9
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 19198 / Rsym value: 0.795 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.787 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.042 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17814 1877 1 %RANDOM
Rwork0.15114 ---
all0.1514 185716 --
obs0.1514 185716 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.066 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.06 Å2
2--1.53 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4747 0 170 574 5491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225146
X-RAY DIFFRACTIONr_bond_other_d0.0030.023328
X-RAY DIFFRACTIONr_angle_refined_deg1.9411.9747048
X-RAY DIFFRACTIONr_angle_other_deg1.1153.0037993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1215603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13625.018277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35815764
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.361521
X-RAY DIFFRACTIONr_chiral_restr0.1510.2768
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025766
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021082
X-RAY DIFFRACTIONr_nbd_refined0.2240.2959
X-RAY DIFFRACTIONr_nbd_other0.2030.23635
X-RAY DIFFRACTIONr_nbtor_refined0.1910.22629
X-RAY DIFFRACTIONr_nbtor_other0.1010.22696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2446
X-RAY DIFFRACTIONr_metal_ion_refined0.1010.223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2050.229
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0880.21
X-RAY DIFFRACTIONr_mcbond_it2.0511.52955
X-RAY DIFFRACTIONr_mcbond_other0.8741.51217
X-RAY DIFFRACTIONr_mcangle_it2.96324772
X-RAY DIFFRACTIONr_scbond_it4.37932308
X-RAY DIFFRACTIONr_scangle_it6.0464.52276
X-RAY DIFFRACTIONr_rigid_bond_restr2.20539104
X-RAY DIFFRACTIONr_sphericity_free12.7885579
X-RAY DIFFRACTIONr_sphericity_bonded4.16958321
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 150 -
Rwork0.31 13370 -
obs--97.34 %

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