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- PDB-8rr2: 3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto... -

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Basic information

Entry
Database: PDB / ID: 8rr2
Title3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto-glucose
Components3-keto-disaccharide hydrolase domain-containing protein
KeywordsLYASE / Product Complex
Function / homology3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / : / Uncharacterized protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsPfeiffer, M. / Kastner, K. / Oberdorfer, G. / Nidetzky, B.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science Fund Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Enzyme Machinery for Bacterial Glucoside Metabolism through a Conserved Non-hydrolytic Pathway.
Authors: Kastner, K. / Bitter, J. / Pfeiffer, M. / Grininger, C. / Oberdorfer, G. / Pavkov-Keller, T. / Weber, H. / Nidetzky, B.
History
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification
Revision 1.2Oct 30, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-keto-disaccharide hydrolase domain-containing protein
B: 3-keto-disaccharide hydrolase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,68910
Polymers61,9752
Non-polymers7158
Water10,142563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-1 kcal/mol
Surface area21050 Å2
Unit cell
Length a, b, c (Å)76.270, 79.880, 103.820
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 , 1 types, 2 molecules AB

#1: Protein 3-keto-disaccharide hydrolase domain-containing protein


Mass: 30987.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BSIG_4447, Btheta7330_00884
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0P0FHP3

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Non-polymers , 5 types, 571 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / 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
#5: Chemical ChemComp-A1H2X / (2~{R},3~{R},5~{S},6~{S})-2-(hydroxymethyl)-3,5,6-tris(oxidanyl)oxan-4-one


Mass: 178.140 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O6 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5 35% pentaerythritol ethoxylate, 6% polyvinlypirolidone Soaking for 90 minutes with 20 mM 3-keto-sucrose

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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 X 16M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03323 Å / Relative weight: 1
ReflectionResolution: 1.74→48.71 Å / Num. obs: 65902 / % possible obs: 99.83 % / Redundancy: 13.5 % / Biso Wilson estimate: 25.57 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.2064 / Rpim(I) all: 0.0767 / Rrim(I) all: 0.2847 / Net I/av σ(I): 8.03 / Net I/σ(I): 8.03
Reflection shellResolution: 1.78→1.844 Å / Mean I/σ(I) obs: 0.62 / Num. unique obs: 83345 / CC1/2: 0.416 / CC star: 0.766 / % possible all: 99.75

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 1.74→48.71 Å / SU ML: 0.2165 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.3312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1972 2098 3.18 %
Rwork0.1665 63780 -
obs0.1674 65878 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.23 Å2
Refinement stepCycle: LAST / Resolution: 1.74→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 44 563 4628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01054189
X-RAY DIFFRACTIONf_angle_d1.10785672
X-RAY DIFFRACTIONf_chiral_restr0.0754579
X-RAY DIFFRACTIONf_plane_restr0.0072749
X-RAY DIFFRACTIONf_dihedral_angle_d13.58651522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.32881360.31444138X-RAY DIFFRACTION98.89
1.78-1.820.3281380.28794223X-RAY DIFFRACTION99.95
1.82-1.870.34061380.28374193X-RAY DIFFRACTION99.91
1.87-1.930.29151380.25544186X-RAY DIFFRACTION99.95
1.93-1.990.25451390.21484222X-RAY DIFFRACTION99.91
1.99-2.060.22971380.18064204X-RAY DIFFRACTION99.84
2.06-2.140.20381400.16984229X-RAY DIFFRACTION99.98
2.14-2.240.2171390.1714220X-RAY DIFFRACTION99.98
2.24-2.360.21941390.1654250X-RAY DIFFRACTION99.95
2.36-2.510.21951400.15934232X-RAY DIFFRACTION99.91
2.51-2.70.19191400.15094257X-RAY DIFFRACTION99.84
2.7-2.970.16321400.16144290X-RAY DIFFRACTION99.91
2.97-3.40.16521410.15484274X-RAY DIFFRACTION100
3.4-4.280.17351430.13584349X-RAY DIFFRACTION99.98
4.28-48.710.16991490.15144513X-RAY DIFFRACTION99.85

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