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- PDB-9fz3: Crystal structure of K38 amylase from Bacillus sp. strain KSM-K38... -

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Basic information

Entry
Database: PDB / ID: 9fz3
TitleCrystal structure of K38 amylase from Bacillus sp. strain KSM-K38 covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe
ComponentsAmylase
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / AMYLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / calcium ion binding
Similarity search - Function
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 / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / OCTAN-1-OL / Chem-PBW / Amylase
Similarity search - Component
Biological speciesBacillus sp. KSM-K38 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsPickles, I.B. / Moroz, O. / Davies, G.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)951231European Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Precision Activity-Based alpha-Amylase Probes for Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes.
Authors: Pickles, I.B. / Chen, Y. / Moroz, O. / Brown, H.A. / de Boer, C. / Armstrong, Z. / McGregor, N.G.S. / Artola, M. / Codee, J.D.C. / Koropatkin, N.M. / Overkleeft, H.S. / Davies, G.J.
History
DepositionJul 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,3188
Polymers57,5231
Non-polymers7957
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-21 kcal/mol
Surface area16870 Å2
Unit cell
Length a, b, c (Å)132.486, 132.486, 132.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-930-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Amylase


Mass: 57523.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. KSM-K38 (bacteria) / Gene: amyK38 / Production host: Escherichia coli (E. coli) / References: UniProt: Q93I48
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 238 molecules

#3: Chemical ChemComp-PBW / (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Mass: 194.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5, 34% (w/v) PEG 4000 and 1 mM 4'-octylamine-alpha-D-maltotriose epicyclophellitol (compound 2a).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.02→66.24 Å / Num. obs: 51019 / % possible obs: 100 % / Redundancy: 41.1 % / CC1/2: 1 / Rmerge(I) obs: 0.15 / Net I/σ(I): 17.2
Reflection shellResolution: 2.02→2.07 Å / Num. unique obs: 3775 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→66.24 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.724 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24173 2598 5.1 %RANDOM
Rwork0.20126 ---
obs0.20336 48345 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.529 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.02→66.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 43 232 4165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124072
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163422
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.7825531
X-RAY DIFFRACTIONr_angle_other_deg0.5811.7687849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3345478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.62520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00710576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2620.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021077
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0754.5751916
X-RAY DIFFRACTIONr_mcbond_other4.0664.5741915
X-RAY DIFFRACTIONr_mcangle_it5.1498.222392
X-RAY DIFFRACTIONr_mcangle_other5.158.2212393
X-RAY DIFFRACTIONr_scbond_it4.1874.7922156
X-RAY DIFFRACTIONr_scbond_other4.1874.7922153
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.678.6743137
X-RAY DIFFRACTIONr_long_range_B_refined6.92847.34842
X-RAY DIFFRACTIONr_long_range_B_other6.91346.274807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 208 -
Rwork0.37 3530 -
obs--99.55 %

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