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- PDB-8dhe: Tannerella forsythia beta-glucuronidase (mL1) -

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Basic information

Entry
Database: PDB / ID: 8dhe
TitleTannerella forsythia beta-glucuronidase (mL1)
ComponentsGlycosyl hydrolase family 2, sugar bindingdomain protein
KeywordsHYDROLASE / Glycoside hydrolase family 2 / TIM barrel domain
Function / homology
Function and homology information


carbohydrate catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Glycosyl hydrolase family 2, sugar bindingdomain protein
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsLietzan, A.D. / Redinbo, M.R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)TR002489 United States
CitationJournal: Sci Adv / Year: 2023
Title: Microbial beta-glucuronidases drive human periodontal disease etiology.
Authors: Lietzan, A.D. / Simpson, J.B. / Walton, W.G. / Jariwala, P.B. / Xu, Y. / Boynton, M.H. / Liu, J. / Redinbo, M.R.
History
DepositionJun 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 2, sugar bindingdomain protein
B: Glycosyl hydrolase family 2, sugar bindingdomain protein
C: Glycosyl hydrolase family 2, sugar bindingdomain protein
D: Glycosyl hydrolase family 2, sugar bindingdomain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,18618
Polymers317,3034
Non-polymers88314
Water13,313739
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15110 Å2
ΔGint-57 kcal/mol
Surface area89420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.442, 139.647, 109.821
Angle α, β, γ (deg.)90.000, 94.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycosyl hydrolase family 2, sugar bindingdomain protein


Mass: 79325.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: TFKS16_2216 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E4FP39
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 739 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 51.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 6% (w/v) PEG8000, 12% (v/v) ethylene glycol, 5% (v/v) glycerol, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 15, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.2→109.48 Å / Num. obs: 147811 / % possible obs: 96.9 % / Redundancy: 2 % / Biso Wilson estimate: 33.39 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.087 / Rrim(I) all: 0.129 / Net I/σ(I): 4.6 / Num. measured all: 288354
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.9 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.240.6621360872060.5910.6060.90.895.8
12.05-109.480.01617869480.9990.0150.02218.196.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDS20200131data reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMG

3cmg


Resolution: 2.2→51.71 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 2007 1.36 %
Rwork0.205 145728 -
obs0.2055 147735 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.17 Å2 / Biso mean: 37.2839 Å2 / Biso min: 17.07 Å2
Refinement stepCycle: final / Resolution: 2.2→51.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21185 0 52 739 21976
Biso mean--40.04 35.16 -
Num. residues----2637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.34921440.3278102291037396
2.26-2.320.36541390.317103221046196
2.32-2.380.37611380.3111103531049196
2.38-2.460.32131580.2887104071056597
2.46-2.550.36321260.2792104311055797
2.55-2.650.35211500.2688103741052497
2.65-2.770.31371460.2552103771052397
2.77-2.920.30871320.2395104641059697
2.92-3.10.27851520.2242103961054897
3.1-3.340.25591340.2024104741060897
3.34-3.680.23451460.1874104141056097
3.68-4.210.17891520.1534104771062997
4.21-5.30.15561400.1368104211056196
5.3-51.710.18251500.1651105891073997

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