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- PDB-8dhl: Tannerella forsythia beta-glucuronidase (L2) -

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Basic information

Entry
Database: PDB / ID: 8dhl
TitleTannerella forsythia beta-glucuronidase (L2)
ComponentsGlycosyl hydrolase family 2, sugar binding domain 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
Malectin domain / Malectin domain / 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 ...Malectin domain / Malectin domain / 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 binding domain protein
Similarity search - Component
Biological speciesTannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 binding domain protein
B: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,30317
Polymers201,5392
Non-polymers76515
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7710 Å2
ΔGint-37 kcal/mol
Surface area58490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.983, 119.209, 209.883
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycosyl hydrolase family 2, sugar binding domain protein / Beta-glucuronidase


Mass: 100769.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: G8UKC1
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: 6% (w/v) PEG8000, 8% (v/v) ethylene glycol, 2% (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: 0.96802 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96802 Å / Relative weight: 1
ReflectionResolution: 2.3→103.66 Å / Num. obs: 87551 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.081 / Rrim(I) all: 0.21 / Net I/σ(I): 7 / Num. measured all: 575179 / Scaling rejects: 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.346.70.5632955044050.8590.2340.613.3100
12.39-103.665.80.11938916730.9850.0570.13310.799.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4489refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UJ6

5uj6


Resolution: 2.3→78.77 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 2000 2.29 %
Rwork0.1695 85447 -
obs0.1704 87447 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.66 Å2 / Biso mean: 22.2024 Å2 / Biso min: 9.79 Å2
Refinement stepCycle: final / Resolution: 2.3→78.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13216 0 42 778 14036
Biso mean--28.4 24.32 -
Num. residues----1680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.360.31621400.221459986138
2.36-2.420.22931410.199960046145
2.42-2.490.22691410.191560336174
2.49-2.570.23811400.184859966136
2.57-2.660.2571420.185560416183
2.66-2.770.24251420.193660646206
2.77-2.90.24211410.202460566197
2.9-3.050.22561420.190860566198
3.05-3.240.23981430.183961136256
3.24-3.490.22941430.174960986241
3.49-3.840.21221440.163261426286
3.84-4.40.15641430.133361476290
4.4-5.540.14571470.125262356382
5.54-78.770.18211510.159864646615
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0524-0.0046-0.04170.4483-0.09990.0514-0.0173-0.0005-0.00410.0019-0.0107-0.04060.01370.004-0.00540.0918-0.00640.00480.10860.02210.0845-6.881646.3084134.4316
20.0854-0.0873-0.01720.393-0.04010.06410.00730.01990.0046-0.04680.0010.1099-0.0002-0.0184-0.00160.0889-0.0134-0.0170.11820.02740.0895-34.46169.9252124.6689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 28 through 885)A28 - 885
2X-RAY DIFFRACTION2(chain 'B' and resid 29 through 885)B29 - 885

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