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- PDB-8dhv: Treponema lecithinolyticum beta-glucuronidase -

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Basic information

Entry
Database: PDB / ID: 8dhv
TitleTreponema lecithinolyticum beta-glucuronidase
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
KeywordsHYDROLASE / Glycoside hydrolase family 2 / TIM barrel domain
Function / homology:
Function and homology information
Biological speciesTreponema lecithinolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 28, 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

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Assembly

Deposited unit
A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,06420
Polymers144,4672
Non-polymers1,59718
Water17,691982
1
A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules

A: Glycosyl hydrolase family 2, TIM barrel domain protein
B: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,12840
Polymers288,9344
Non-polymers3,19436
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area27170 Å2
ΔGint-568 kcal/mol
Surface area73070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.302, 94.302, 287.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glycosyl hydrolase family 2, TIM barrel domain protein / beta-glucuronidase


Mass: 72233.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema lecithinolyticum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: U2KI81, beta-glucuronidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#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.: 982 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2 M ammonium sulfate, 0.1 M MOPS, 4% (v/v) MPD

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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: Jun 18, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 1.6→89.62 Å / Num. obs: 170930 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 23.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.028 / Rrim(I) all: 0.097 / Net I/σ(I): 13.1 / Num. measured all: 1896978 / Scaling rejects: 4
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
1.6-1.635.41.8174519183550.5240.8482.0110.999.8
8.76-89.6210.10.0481274812630.9980.0150.0544.8100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BJQ

6bjq


Resolution: 1.6→49.15 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1997 1.17 %
Rwork0.1665 168477 -
obs0.1669 170474 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.09 Å2 / Biso mean: 29.5718 Å2 / Biso min: 16.35 Å2
Refinement stepCycle: final / Resolution: 1.6→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9523 0 89 982 10594
Biso mean--43.59 35.98 -
Num. residues----1195
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 (%)
1.6-1.640.31881380.3273118111194999
1.64-1.680.31771430.29211195712100100
1.68-1.730.29661400.25321188212022100
1.73-1.790.28271420.22361190512047100
1.79-1.850.23211420.19291198212124100
1.85-1.930.22221420.19971192712069100
1.93-2.020.22491420.16971198312125100
2.02-2.120.18531410.16581198012121100
2.12-2.260.19861440.16091203112175100
2.26-2.430.1811420.15861206012202100
2.43-2.670.19491440.16391212012264100
2.67-3.060.211450.17031219312338100
3.06-3.860.1891390.1481117831192296
3.86-49.150.1591530.14471286313016100
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)
10.1841-0.09390.05150.1994-0.03790.49940.0017-0.0337-0.01820.05110.02230.03460.0461-0.02900.2041-0.0010.00770.18930.01390.229628.797819.4226.4037
20.273-0.0609-0.01990.25220.05840.5837-0.014-0.01980.02920.04360.0446-0.0244-0.02590.22130.00010.1574-0.0168-0.0110.2935-0.02470.210162.790130.69214.9022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 623)A16 - 623
2X-RAY DIFFRACTION2(chain 'B' and resid 17 through 624)B17 - 624

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