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- PDB-8e72: Treponema lecithinolyticum beta-glucuronidase in complex with a c... -

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Basic information

Entry
Database: PDB / ID: 8.0E+72
TitleTreponema lecithinolyticum beta-glucuronidase in complex with a ciprofloxacin-glucuronide conjugate
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
KeywordsHYDROLASE / Glycoside hydrolase family 2 / TIM barrel domain
Function / homologyChem-USL / :
Function and homology information
Biological speciesTreponema lecithinolyticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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
DepositionAug 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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)145,6008
Polymers144,2052
Non-polymers1,3956
Water11,403633
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)291,19916
Polymers288,4094
Non-polymers2,79012
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area19140 Å2
ΔGint-193 kcal/mol
Surface area73880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.406, 94.406, 288.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 72102.258 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
#2: Chemical ChemComp-USL / 3-carboxy-1-cyclopropyl-6-fluoro-7-(4-beta-D-glucopyranuronosyl-3,4-dihydropyrazin-1(2H)-yl)-4-oxo-1,4-dihydroquinoline


Mass: 505.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H24FN3O9
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M ammonium sulfate, 0.1 M MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→89.71 Å / Num. obs: 95127 / % possible obs: 99.2 % / Redundancy: 8.7 % / Biso Wilson estimate: 35.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.053 / Rrim(I) all: 0.159 / Net I/σ(I): 9.8 / Num. measured all: 824185 / Scaling rejects: 54
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
1.95-2.058.92.219123853138390.4870.7712.3531.1100
6.16-89.717.90.042585832620.9990.0150.04334.197.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DHV

8dhv


Resolution: 1.95→66.76 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 2000 2.11 %
Rwork0.1843 --
obs0.1849 94955 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→66.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9424 0 92 633 10149
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089871
X-RAY DIFFRACTIONf_angle_d1.07813449
X-RAY DIFFRACTIONf_dihedral_angle_d14.4223527
X-RAY DIFFRACTIONf_chiral_restr0.0631461
X-RAY DIFFRACTIONf_plane_restr0.0081723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.34781420.30546613X-RAY DIFFRACTION100
2-2.050.29261430.26756624X-RAY DIFFRACTION100
2.05-2.110.32631420.24926586X-RAY DIFFRACTION100
2.11-2.180.27391430.24896633X-RAY DIFFRACTION100
2.18-2.260.39761400.31656549X-RAY DIFFRACTION99
2.26-2.350.3031420.2416586X-RAY DIFFRACTION99
2.35-2.450.28241420.20886624X-RAY DIFFRACTION100
2.45-2.580.23381430.19416634X-RAY DIFFRACTION100
2.58-2.750.23121430.19766671X-RAY DIFFRACTION100
2.75-2.960.25881440.20526683X-RAY DIFFRACTION99
2.96-3.260.2211450.18526691X-RAY DIFFRACTION99
3.26-3.730.2061350.16416307X-RAY DIFFRACTION93
3.73-4.690.14081460.12986772X-RAY DIFFRACTION98
4.69-66.760.15841500.16056982X-RAY DIFFRACTION97

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