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- PDB-6yq9: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol ep... -

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Basic information

Entry
Database: PDB / ID: 6yq9
TitleTaka-amylase in complex with alpha-glucosyl epi-cyclophellitol epoxide inhibitor
ComponentsAlpha-amylase
KeywordsHYDROLASE / Inhibitor / Complex / Amylase
Function / homology
Function and homology information


alpha-amylase / carbohydrate catabolic process / alpha-amylase activity / 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
Chem-5QP / Alpha-amylase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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 10, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 24, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Jan 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

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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)111,14512
Polymers109,6942
Non-polymers1,45110
Water14,682815
1
AAA: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5105
Polymers54,8471
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6357
Polymers54,8471
Non-polymers7886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-11 kcal/mol
Surface area31780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.214, 103.100, 75.374
Angle α, β, γ (deg.)90.000, 103.632, 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 / N-Acetylglucosamine


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
#4: Sugar ChemComp-5QP / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(1~{R},2~{S},3~{R},5~{S},6~{R})-2-(hydroxymethyl)-3,5,6-tris(oxida nyl)cyclohexyl]oxy-oxane-3,4,5-triol / gluosyl epi-cyclophellitol (bound form) / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucoside / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl D-glucoside / (1R,2R,3S,5R,6S)-2,3,5-trihydroxy-6-(hydroxymethyl)cyclohexyl glucoside


Type: D-saccharide / Mass: 340.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C13H24O10 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 3 types, 821 molecules

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


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 815 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.24 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
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: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.55→103.1 Å / Num. obs: 139975 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.995 / Net I/σ(I): 11.8
Reflection shellResolution: 1.55→1.58 Å / Num. unique obs: 6883 / CC1/2: 0.874

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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: 1.55→73.358 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.069
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1736 6862 4.904 %
Rwork0.1463 --
all0.148 --
obs-139928 99.86 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.912 Å2
Baniso -1Baniso -2Baniso -3
1--0.071 Å20 Å2-0.366 Å2
2--1.913 Å2-0 Å2
3----1.489 Å2
Refinement stepCycle: LAST / Resolution: 1.55→73.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7368 0 92 815 8275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0137785
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176695
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.65710654
X-RAY DIFFRACTIONr_angle_other_deg2.5351.58715624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.3935.211994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63224.34371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.018151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9211521
X-RAY DIFFRACTIONr_chiral_restr0.1050.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.029660
X-RAY DIFFRACTIONr_gen_planes_other0.0220.021605
X-RAY DIFFRACTIONr_nbd_refined0.2310.21583
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.26540
X-RAY DIFFRACTIONr_nbtor_refined0.1780.23977
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23191
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2658
X-RAY DIFFRACTIONr_metal_ion_refined0.0590.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0640.28
X-RAY DIFFRACTIONr_nbd_other0.1810.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.222
X-RAY DIFFRACTIONr_mcbond_it1.4481.6883876
X-RAY DIFFRACTIONr_mcbond_other1.4461.6873875
X-RAY DIFFRACTIONr_mcangle_it2.0312.534866
X-RAY DIFFRACTIONr_mcangle_other2.0312.5314867
X-RAY DIFFRACTIONr_scbond_it2.3511.8273909
X-RAY DIFFRACTIONr_scbond_other2.3511.8273910
X-RAY DIFFRACTIONr_scangle_it3.4182.675788
X-RAY DIFFRACTIONr_scangle_other3.4182.6715789
X-RAY DIFFRACTIONr_lrange_it4.18620.6499305
X-RAY DIFFRACTIONr_lrange_other4.06320.2339135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.2655050.2269805X-RAY DIFFRACTION99.5654
1.59-1.6340.2364770.2069571X-RAY DIFFRACTION99.9204
1.634-1.6810.234890.1969295X-RAY DIFFRACTION99.6943
1.681-1.7330.2084590.1819001X-RAY DIFFRACTION99.9577
1.733-1.790.2034770.1648748X-RAY DIFFRACTION99.8917
1.79-1.8520.1994510.1518477X-RAY DIFFRACTION99.7653
1.852-1.9220.1924150.1528144X-RAY DIFFRACTION99.8483
1.922-2.0010.1853760.1467915X-RAY DIFFRACTION99.9036
2.001-2.090.1743980.147575X-RAY DIFFRACTION99.9875
2.09-2.1920.1713570.147218X-RAY DIFFRACTION100
2.192-2.310.1633880.1316853X-RAY DIFFRACTION100
2.31-2.450.1553310.1296534X-RAY DIFFRACTION100
2.45-2.6190.1612960.1276120X-RAY DIFFRACTION100
2.619-2.8290.1662890.135729X-RAY DIFFRACTION99.9668
2.829-3.0990.1722680.1395243X-RAY DIFFRACTION100
3.099-3.4640.1572980.154724X-RAY DIFFRACTION100
3.464-3.9990.151980.1374201X-RAY DIFFRACTION99.9546
3.999-4.8960.1381720.1223587X-RAY DIFFRACTION99.9468
4.896-6.9170.1641430.1642763X-RAY DIFFRACTION99.9656
6.917-73.3580.202750.1551564X-RAY DIFFRACTION100

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