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- PDB-9fbe: 3-keto-glycoside eliminase/hydratase in komplex with 2-hydroxy-3-... -

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Basic information

Entry
Database: PDB / ID: 9fbe
Title3-keto-glycoside eliminase/hydratase in komplex with 2-hydroxy-3-keto-glucal
ComponentsProbable secreted glycosyl hydrolase
KeywordsLYASE / Product Complex
Function / homologyalpha-3'-ketoglucosidase / 3-keto-disaccharide hydrolase / 3-keto-alpha-glucoside-1,2-lyase-like domain / hydrolase activity, acting on glycosyl bonds / Prokaryotic membrane lipoprotein lipid attachment site profile. / plasma membrane / : / alpha-D-glucopyranose / 3-keto-disaccharide hydrolase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsPfeiffer, M. / Kastner, K. / Oberdorfer, G. / Nidetzky, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: To Be Published
Title: 3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto-glucose
Authors: Pfeiffer, M. / Oberdorfer, G. / Nidetzky, B. / Kastner, K.
History
DepositionMay 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable secreted glycosyl hydrolase
A: Probable secreted glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3559
Polymers61,6502
Non-polymers7057
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-1 kcal/mol
Surface area21120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.348, 80.926, 103.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein / Sugars , 2 types, 3 molecules BA

#1: Protein Probable secreted glycosyl hydrolase


Mass: 30825.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2157
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8A5T1
#5: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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, 538 molecules

#2: Chemical ChemComp-A1IBU / 2-hydroxy-3-keto-glucal / (2~{R},3~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-2,3-dihydropyran-4-one


Mass: 160.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5, 32% v/v pentaerythritol ethoxylate 15/4, 6% w/v polyvinylpirolidone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03323 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.93→40.46 Å / Num. obs: 48829 / % possible obs: 99.79 % / Redundancy: 14 % / Biso Wilson estimate: 33.93 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1595 / Rrim(I) all: 0.1656 / Net I/σ(I): 11.79
Reflection shellResolution: 1.93→1.97 Å / Num. unique obs: 4787 / CC1/2: 0.534

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→40.46 Å / SU ML: 0.229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 2507 5.14 %
Rwork0.1698 46297 -
obs0.1721 48804 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.46 Å2
Refinement stepCycle: LAST / Resolution: 1.93→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 44 532 4600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01364180
X-RAY DIFFRACTIONf_angle_d1.27075657
X-RAY DIFFRACTIONf_chiral_restr0.0824578
X-RAY DIFFRACTIONf_plane_restr0.0084745
X-RAY DIFFRACTIONf_dihedral_angle_d13.61981506
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.970.33941290.30032512X-RAY DIFFRACTION98.77
1.97-2.010.29561110.26492577X-RAY DIFFRACTION99.89
2.01-2.050.28381540.23982518X-RAY DIFFRACTION99.89
2.05-2.10.26141190.21842540X-RAY DIFFRACTION100
2.1-2.150.25731220.21712550X-RAY DIFFRACTION100
2.15-2.210.25781420.20932564X-RAY DIFFRACTION100
2.21-2.280.24811300.1992554X-RAY DIFFRACTION99.93
2.28-2.350.2431210.19582572X-RAY DIFFRACTION99.96
2.35-2.440.24891270.19562573X-RAY DIFFRACTION99.89
2.44-2.530.24821440.18592569X-RAY DIFFRACTION99.93
2.53-2.650.26391600.18332524X-RAY DIFFRACTION99.78
2.65-2.790.23031470.19322557X-RAY DIFFRACTION99.96
2.79-2.960.30251540.18912549X-RAY DIFFRACTION100
2.96-3.190.22821480.18122580X-RAY DIFFRACTION99.56
3.19-3.510.20281440.16182562X-RAY DIFFRACTION99.08
3.51-4.020.16721360.13412622X-RAY DIFFRACTION100
4.02-5.060.15691550.11992633X-RAY DIFFRACTION100
5.06-40.460.17041640.15782741X-RAY DIFFRACTION99.93

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