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- PDB-6yqa: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol az... -

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Basic information

Entry
Database: PDB / ID: 6yqa
TitleTaka-amylase in complex with alpha-glucosyl epi-cyclophellitol aziridine inhibitor
ComponentsAlpha-amylase
KeywordsHYDROLASE / Inhibitor / Complex / Amylase
Function / homology
Function and homology information


alpha-amylase / alpha-amylase activity / carbohydrate catabolic process / calcium ion binding
Similarity search - Function
Alpha-amylase, domain C / Alpha-amylase, domain C / Alpha-amylase-like / Alpha amylase / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
alpha-D-glucopyranose / Chem-P9Q / Alpha-amylase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsArmstrong, Z. / Chen, Y. / Artola, M. / Overkleeft, H. / Davies, G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001162/1 United Kingdom
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Activity-Based Protein Profiling of Retaining alpha-Amylases in Complex Biological Samples.
Authors: Chen, Y. / Armstrong, Z. / Artola, M. / Florea, B.I. / Kuo, C.L. / de Boer, C. / Rasmussen, M.S. / Abou Hachem, M. / van der Marel, G.A. / Codee, J.D.C. / Aerts, J.M.F.G. / Davies, G.J. / Overkleeft, H.S.
History
DepositionApr 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Alpha-amylase
BBB: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,49615
Polymers109,6942
Non-polymers1,80213
Water9,350519
1
AAA: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7177
Polymers54,8471
Non-polymers8706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7798
Polymers54,8471
Non-polymers9327
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.684, 103.320, 75.508
Angle α, β, γ (deg.)90.000, 103.827, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein Alpha-amylase


Mass: 54846.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01097160 / Production host: Aspergillus oryzae (mold) / References: UniProt: A0A1S9DH83, alpha-amylase

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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: 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, 528 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-P9Q / (1~{S},2~{R},3~{R},4~{R},5~{R})-5-(8-azanyloctylamino)-4-(hydroxymethyl)cyclohexane-1,2,3-triol


Mass: 304.426 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32N2O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium citrate pH 5.6, 18% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979499 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979499 Å / Relative weight: 1
ReflectionResolution: 1.67→103.32 Å / Num. obs: 113249 / % possible obs: 100 % / Redundancy: 4.2 % / CC1/2: 0.997 / Net I/σ(I): 9.6
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 5574 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7taa

7taa


Resolution: 1.67→73.427 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.093
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.201 5597 4.944 %
Rwork0.1719 --
all0.173 --
obs-113215 99.93 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.078 Å2
Baniso -1Baniso -2Baniso -3
1--0.517 Å2-0 Å2-1.014 Å2
2--4.26 Å2-0 Å2
3----2.893 Å2
Refinement stepCycle: LAST / Resolution: 1.67→73.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 107 519 7994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0137712
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176664
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.6610540
X-RAY DIFFRACTIONr_angle_other_deg2.451.59215538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.59124.247372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.219151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1991521
X-RAY DIFFRACTIONr_chiral_restr0.0870.21038
X-RAY DIFFRACTIONr_gen_planes_refined0.010.028722
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021585
X-RAY DIFFRACTIONr_nbd_refined0.2090.21526
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.26431
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23910
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.23000
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2523
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0850.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1010.210
X-RAY DIFFRACTIONr_nbd_other0.1690.237
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0670.28
X-RAY DIFFRACTIONr_mcbond_it1.9412.7213826
X-RAY DIFFRACTIONr_mcbond_other1.9382.723825
X-RAY DIFFRACTIONr_mcangle_it2.5224.0724786
X-RAY DIFFRACTIONr_mcangle_other2.5224.0734787
X-RAY DIFFRACTIONr_scbond_it2.5612.8713886
X-RAY DIFFRACTIONr_scbond_other2.5612.8723887
X-RAY DIFFRACTIONr_scangle_it3.6784.2285754
X-RAY DIFFRACTIONr_scangle_other3.6784.2285755
X-RAY DIFFRACTIONr_lrange_it4.36632.1619000
X-RAY DIFFRACTIONr_lrange_other4.334328911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.7130.3534080.3627950X-RAY DIFFRACTION99.8328
1.713-1.760.3433850.3337737X-RAY DIFFRACTION99.9631
1.76-1.8110.3244160.2997492X-RAY DIFFRACTION99.9874
1.811-1.8670.2793930.2677272X-RAY DIFFRACTION99.9739
1.867-1.9280.2573710.2297107X-RAY DIFFRACTION99.9465
1.928-1.9960.2343500.2066877X-RAY DIFFRACTION99.9862
1.996-2.0710.2263590.1766583X-RAY DIFFRACTION99.9856
2.071-2.1560.2013290.1646355X-RAY DIFFRACTION99.9551
2.156-2.2520.2022920.1576151X-RAY DIFFRACTION99.9845
2.252-2.3610.1992850.155899X-RAY DIFFRACTION99.9838
2.361-2.4890.1982930.1495500X-RAY DIFFRACTION99.9827
2.489-2.640.1882700.1525287X-RAY DIFFRACTION99.964
2.64-2.8220.2032470.1584959X-RAY DIFFRACTION99.9808
2.822-3.0480.1862450.1564598X-RAY DIFFRACTION100
3.048-3.3390.1992280.1654229X-RAY DIFFRACTION100
3.339-3.7320.1951780.1613876X-RAY DIFFRACTION99.9507
3.732-4.3090.1641920.1423377X-RAY DIFFRACTION100
4.309-5.2750.1381560.1252870X-RAY DIFFRACTION100
5.275-7.450.1821210.1592255X-RAY DIFFRACTION99.8739
7.45-73.4270.153790.1431244X-RAY DIFFRACTION99.8491

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