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- PDB-9fyz: Crystal structure of SusA amylase from Bacteroides thetaiotaomicr... -

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Basic information

Entry
Database: PDB / ID: 9fyz
TitleCrystal structure of SusA amylase from Bacteroides thetaiotaomicron covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe
ComponentsNeopullulanase SusA
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / AMYLASE
Function / homology
Function and homology information


neopullulanase activity / neopullulanase / starch catabolic process / periplasmic space / metal ion binding / plasma membrane
Similarity search - Function
Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase, C-terminal / Cyclomaltodextrinase, N-terminal / Cyclo-malto-dextrinase C-terminal domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Immunoglobulin E-set / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IMIDAZOLE / OCTAN-1-OL / Chem-PBW / Neopullulanase SusA
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 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

Downloads & links

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Assembly

Deposited unit
A: Neopullulanase SusA
B: Neopullulanase SusA
C: Neopullulanase SusA
D: Neopullulanase SusA
E: Neopullulanase SusA
F: Neopullulanase SusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,74547
Polymers423,5656
Non-polymers5,18041
Water12,863714
1
A: Neopullulanase SusA
hetero molecules

A: Neopullulanase SusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,09718
Polymers141,1882
Non-polymers1,90816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6870 Å2
ΔGint-16 kcal/mol
Surface area42140 Å2
2
B: Neopullulanase SusA
hetero molecules

B: Neopullulanase SusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,82014
Polymers141,1882
Non-polymers1,63212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6310 Å2
ΔGint-43 kcal/mol
Surface area42810 Å2
3
C: Neopullulanase SusA
hetero molecules

E: Neopullulanase SusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,95816
Polymers141,1882
Non-polymers1,77014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area5830 Å2
ΔGint-50 kcal/mol
Surface area41720 Å2
4
D: Neopullulanase SusA
F: Neopullulanase SusA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,82815
Polymers141,1882
Non-polymers1,64013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-40 kcal/mol
Surface area41990 Å2
Unit cell
Length a, b, c (Å)105.978, 105.978, 753.691
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11F-821-

HOH

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Components

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Protein / Sugars , 2 types, 12 molecules ABCDEF

#1: Protein
Neopullulanase SusA / Starch-utilization system protein A


Mass: 70594.195 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: susA, BT_3704 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1G0, neopullulanase
#2: Polysaccharide
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 6
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, 749 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.: 6 / 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.: 5 / Source method: obtained synthetically / Formula: C8H18O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 714 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 30 mM sodium fluoride, 30 mM sodium bromide, 30 mM sodium iodide, 50 mM MES pH 6.5, 50 mM imidazole, 20% (v/v) glycerol and 10% (w/v) PEG 4000

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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: Jan 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.43→58.25 Å / Num. obs: 212465 / % possible obs: 100 % / Redundancy: 21.4 % / CC1/2: 1 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 2.43→2.49 Å / Num. unique obs: 10398 / CC1/2: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→58.25 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.168 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28148 9306 5 %RANDOM
Rwork0.2299 ---
obs0.23246 178136 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.021 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å2-0 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.43→58.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27802 0 291 714 28807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01228895
X-RAY DIFFRACTIONr_bond_other_d0.0010.01624999
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.81139285
X-RAY DIFFRACTIONr_angle_other_deg0.5421.75457658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85153541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.9245145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.307104257
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2350.24207
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0234929
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027117
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_it7.4987.33314226
X-RAY DIFFRACTIONr_mcbond_other7.4987.33314226
X-RAY DIFFRACTIONr_mcangle_it10.54413.1617725
X-RAY DIFFRACTIONr_mcangle_other10.54413.1617726
X-RAY DIFFRACTIONr_scbond_it7.5537.47114669
X-RAY DIFFRACTIONr_scbond_other7.5527.47114670
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.79913.5921561
X-RAY DIFFRACTIONr_long_range_B_refined13.15468.1632212
X-RAY DIFFRACTIONr_long_range_B_other13.15368.1632213
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.493 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 719 -
Rwork0.355 12912 -
obs--99.96 %

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