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- PDB-6yqb: Taka-amylase in complex with alpha-glucosyl epi-cyclophellitol cy... -

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Basic information

Entry
Database: PDB / ID: 6yqb
TitleTaka-amylase in complex with alpha-glucosyl epi-cyclophellitol cyclosulfate 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-93Z / alpha-D-glucopyranose / Alpha-amylase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)111,49716
Polymers109,6942
Non-polymers1,80414
Water14,142785
1
AAA: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6877
Polymers54,8471
Non-polymers8406
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Alpha-amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8119
Polymers54,8471
Non-polymers9648
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.583, 102.940, 75.623
Angle α, β, γ (deg.)90.000, 103.812, 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

#3: 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
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / 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, 795 molecules

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


Mass: 62.068 Da / Num. of mol.: 6 / 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-93Z / [(1~{S},2~{R},3~{R},4~{S},5~{R})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate


Mass: 274.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O9S
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 785 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
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: 1.5→59.78 Å / Num. obs: 153290 / % possible obs: 98.7 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 10.3
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 7423 / CC1/2: 0.917

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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: 1.5→59.78 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: FREE R-VALUE / ESU R: 0.066 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1859 7597 4.958 %
Rwork0.1569 --
all0.158 --
obs-153221 98.507 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.852 Å2-0 Å2-0.956 Å2
2--2.794 Å2-0 Å2
3----2.833 Å2
Refinement stepCycle: LAST / Resolution: 1.5→59.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7372 0 108 785 8265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0137780
X-RAY DIFFRACTIONr_bond_other_d0.0370.0176695
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.66110648
X-RAY DIFFRACTIONr_angle_other_deg2.4321.58715628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8975974
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45924.278374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.262151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2151521
X-RAY DIFFRACTIONr_chiral_restr0.0980.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028842
X-RAY DIFFRACTIONr_gen_planes_other0.0180.021601
X-RAY DIFFRACTIONr_nbd_refined0.2230.21502
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2120.26412
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23928
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23035
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2601
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0260.25
X-RAY DIFFRACTIONr_nbd_other0.2130.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1890.221
X-RAY DIFFRACTIONr_mcbond_it1.5892.0843866
X-RAY DIFFRACTIONr_mcbond_other1.5842.0833865
X-RAY DIFFRACTIONr_mcangle_it2.1153.1244850
X-RAY DIFFRACTIONr_mcangle_other2.1153.1254851
X-RAY DIFFRACTIONr_scbond_it2.3742.2393914
X-RAY DIFFRACTIONr_scbond_other2.3742.2383910
X-RAY DIFFRACTIONr_scangle_it3.4433.2815798
X-RAY DIFFRACTIONr_scangle_other3.4433.2815796
X-RAY DIFFRACTIONr_lrange_it4.18225.2319133
X-RAY DIFFRACTIONr_lrange_other4.07224.8318972
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5390.3045500.30810563X-RAY DIFFRACTION96.989
1.539-1.5810.2925490.27310289X-RAY DIFFRACTION97.3852
1.581-1.6270.2464910.24610150X-RAY DIFFRACTION97.6059
1.627-1.6770.2635290.2269808X-RAY DIFFRACTION97.7124
1.677-1.7320.2145370.1939478X-RAY DIFFRACTION97.9462
1.732-1.7930.2284710.1789284X-RAY DIFFRACTION98.2872
1.793-1.860.2034490.1628938X-RAY DIFFRACTION98.3138
1.86-1.9360.24420.1538656X-RAY DIFFRACTION98.4845
1.936-2.0220.2064380.1518258X-RAY DIFFRACTION98.7621
2.022-2.1210.183970.1467928X-RAY DIFFRACTION98.8365
2.121-2.2360.1744030.1397583X-RAY DIFFRACTION99.0942
2.236-2.3710.1744040.1377133X-RAY DIFFRACTION99.2494
2.371-2.5350.1673390.1376771X-RAY DIFFRACTION99.3988
2.535-2.7380.1823420.1416300X-RAY DIFFRACTION99.5653
2.738-2.9990.1832980.155814X-RAY DIFFRACTION99.6901
2.999-3.3530.1992600.1645260X-RAY DIFFRACTION99.8372
3.353-3.8710.1732450.1514686X-RAY DIFFRACTION99.8987
3.871-4.7390.1491900.1273958X-RAY DIFFRACTION100
4.739-6.6950.1411580.1363074X-RAY DIFFRACTION100
6.695-59.8540.1531050.1391693X-RAY DIFFRACTION99.2274

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