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- PDB-9fz0: Crystal structure of SusG from Bacteroides thetaiotaomicron coval... -

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Basic information

Entry
Database: PDB / ID: 9fz0
TitleCrystal structure of SusG from Bacteroides thetaiotaomicron covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe
ComponentsAlpha-amylase SusG
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / AMYLASE
Function / homology
Function and homology information


starch catabolic process / starch binding / alpha-amylase / outer membrane / alpha-amylase activity / oligosaccharide catabolic process / cell outer membrane / calcium ion binding / magnesium ion binding
Similarity search - Function
: / Alpha-amylase SusG, CBM58 domain / : / Alpha-amylase SusG C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. ...: / Alpha-amylase SusG, CBM58 domain / : / Alpha-amylase SusG C-terminal domain / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycosyl hydrolase, all-beta / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / ACETATE ION / IMIDAZOLE / OCTAN-1-OL / Chem-PBW / Alpha-amylase SusG
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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: Alpha-amylase SusG
B: Alpha-amylase SusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,04321
Polymers155,5972
Non-polymers2,44619
Water3,333185
1
A: Alpha-amylase SusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,43814
Polymers77,7991
Non-polymers1,64013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-amylase SusG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6047
Polymers77,7991
Non-polymers8066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.293, 127.293, 129.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Alpha-amylase SusG / Starch-utilization system protein G


Mass: 77798.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: susG, BT_3698 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A1G3, alpha-amylase
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 3
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 , 7 types, 201 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.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C8H18O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-A1ILG / (1~{R},2~{R},3~{S},4~{R},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3,4-triol


Mass: 176.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.36 Å3/Da / Density % sol: 63.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Carboxylic acids (Na-Formate; NH 4-Acetate; Na 3 -Citrate; NaK-Tartrate (racemic); Na-Oxamate), 0.1 M Buffer System 1 (Imidazole; MES (acid)) pH 6.5, 50 % v/v Precipitant Mix 1 (40% ...Details: 0.1 M Carboxylic acids (Na-Formate; NH 4-Acetate; Na 3 -Citrate; NaK-Tartrate (racemic); Na-Oxamate), 0.1 M Buffer System 1 (Imidazole; MES (acid)) pH 6.5, 50 % v/v Precipitant Mix 1 (40% v/v PEG 500* MME; 20 % w/v PEG 20000)

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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: 2.65→64.59 Å / Num. obs: 59811 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.995 / Net I/σ(I): 5.8
Reflection shellResolution: 2.65→2.72 Å / Num. unique obs: 4634 / CC1/2: 0.418

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→63.65 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.928 / SU B: 18.187 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26945 3006 5 %RANDOM
Rwork0.20577 ---
obs0.20887 56734 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.834 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20 Å20 Å2
2---3.76 Å20 Å2
3---7.52 Å2
Refinement stepCycle: 1 / Resolution: 2.65→63.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10067 0 140 185 10392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01210510
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168899
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.80514321
X-RAY DIFFRACTIONr_angle_other_deg0.5681.74220595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14651298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.029526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.854101482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.2170.21561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212452
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022476
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_it7.1557.5125214
X-RAY DIFFRACTIONr_mcbond_other7.1377.5115204
X-RAY DIFFRACTIONr_mcangle_it10.51313.4836494
X-RAY DIFFRACTIONr_mcangle_other10.51213.4846495
X-RAY DIFFRACTIONr_scbond_it6.9387.6815296
X-RAY DIFFRACTIONr_scbond_other6.9177.6795287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.25513.9727810
X-RAY DIFFRACTIONr_long_range_B_refined13.29171.511865
X-RAY DIFFRACTIONr_long_range_B_other13.2971.511866
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 221 -
Rwork0.392 4191 -
obs--99.86 %

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