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- PDB-6ag0: The X-ray Crystallographic Structure of Maltooligosaccharide-form... -

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Basic information

Entry
Database: PDB / ID: 6ag0
TitleThe X-ray Crystallographic Structure of Maltooligosaccharide-forming Amylase from Bacillus stearothermophilus STB04
ComponentsAlpha-amylase
KeywordsSUGAR BINDING PROTEIN / Maltotetraose-forming amylase / Bacillus stearothermophilus STB04
Function / homology
Function and homology information


alpha-amylase activity => GO:0004556 / alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #140 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta ...Elongation Factor Tu (Ef-tu); domain 3 - #140 / 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 / Elongation Factor Tu (Ef-tu); domain 3 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-acarbose / Alpha-amylase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, Z.F. / Li, Y.L. / Ban, X.F. / Zhang, C.Y. / Jin, T.C. / Xie, X.F. / Gu, Z.B. / Li, C.M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722040 China
National Natural Science Foundation of China31571882 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2019
Title: Crystal structure of a maltooligosaccharide-forming amylase from Bacillus stearothermophilus STB04.
Authors: Xie, X. / Li, Y. / Ban, X. / Zhang, Z. / Gu, Z. / Li, C. / Hong, Y. / Cheng, L. / Jin, T. / Li, Z.
History
DepositionAug 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Structure summary / Category: entity / struct / Item: _entity.formula_weight / _struct.title
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Jul 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 / 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_symm_contact / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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.ptnr2_label_asym_id / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_2 / _pdbx_validate_symm_contact.auth_comp_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
C: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,58021
Polymers123,1572
Non-polymers7,42219
Water5,909328
1
A: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,61311
Polymers61,5791
Non-polymers4,03410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,96710
Polymers61,5791
Non-polymers3,3889
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.870, 81.820, 88.780
Angle α, β, γ (deg.)90.00, 105.85, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Alpha-amylase / / Maltohexaose-forming amylase


Mass: 61578.730 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KWY6, alpha-amylase
#2: 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.: 11
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
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-6-deoxy-Glcp4N]{[(4+1)][<C7O4>]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 60% MPD,150 mM NaCl, 1 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018 / Details: MD2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.2→42.189 Å / Num. obs: 53147 / % possible obs: 99.83 % / Redundancy: 6.6 % / Biso Wilson estimate: 33.02 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.06121 / Rrim(I) all: 0.1576 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.279 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.039 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 5332 / CC1/2: 0.7 / Rpim(I) all: 0.4446 / Rrim(I) all: 1.132 / % possible all: 99.79

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KVX

1kvx


Resolution: 2.2→42.189 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.56
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2657 5 %random selection
Rwork0.1673 ---
obs0.1701 53124 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7801 0 492 328 8621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078572
X-RAY DIFFRACTIONf_angle_d1.09311736
X-RAY DIFFRACTIONf_dihedral_angle_d4.174582
X-RAY DIFFRACTIONf_chiral_restr0.0691317
X-RAY DIFFRACTIONf_plane_restr0.0061403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.35761390.27272636X-RAY DIFFRACTION100
2.24-2.28310.33491400.26542667X-RAY DIFFRACTION100
2.2831-2.32970.32231390.24172640X-RAY DIFFRACTION100
2.3297-2.38030.32741390.23272634X-RAY DIFFRACTION100
2.3803-2.43570.29281400.21572651X-RAY DIFFRACTION100
2.4357-2.49660.33521380.21872623X-RAY DIFFRACTION100
2.4966-2.56410.29981390.21442643X-RAY DIFFRACTION100
2.5641-2.63950.25991390.21262661X-RAY DIFFRACTION100
2.6395-2.72470.27331390.20232643X-RAY DIFFRACTION100
2.7247-2.82210.27771390.19082645X-RAY DIFFRACTION100
2.8221-2.9350.25071410.19412666X-RAY DIFFRACTION100
2.935-3.06860.28151380.18482624X-RAY DIFFRACTION100
3.0686-3.23030.22081400.172672X-RAY DIFFRACTION100
3.2303-3.43260.23191410.15212658X-RAY DIFFRACTION100
3.4326-3.69750.19641410.14472669X-RAY DIFFRACTION100
3.6975-4.06930.16931390.12372661X-RAY DIFFRACTION100
4.0693-4.65750.14211400.11262674X-RAY DIFFRACTION100
4.6575-5.86550.16941420.13442682X-RAY DIFFRACTION100
5.8655-42.19710.17641440.15792718X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 26.4553 Å / Origin y: 10.8694 Å / Origin z: 63.7266 Å
111213212223313233
T0.2633 Å2-0.015 Å20.0099 Å2-0.2111 Å2-0.0273 Å2--0.2695 Å2
L0.8232 °2-0.0537 °20.2102 °2-0.0001 °2-0.1022 °2--0.4152 °2
S-0.0166 Å °0.0881 Å °0.0274 Å °-0.0088 Å °-0.0056 Å °-0.0028 Å °0.0051 Å °-0.0138 Å °0.0241 Å °
Refinement TLS groupSelection details: all

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