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- PDB-7kgz: FMN-binding beta-glucuronidase from Roseburia hominis -

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Basic information

Entry
Database: PDB / ID: 7kgz
TitleFMN-binding beta-glucuronidase from Roseburia hominis
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / Beta-glucuronidase / gut microbial enzyme / FMN
Function / homologyFLAVIN MONONUCLEOTIDE
Function and homology information
Biological speciesRoseburia hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWalker, M.E. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137286 United States
CitationJournal: Nat Commun / Year: 2022
Title: Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract.
Authors: Zhang, J. / Walker, M.E. / Sanidad, K.Z. / Zhang, H. / Liang, Y. / Zhao, E. / Chacon-Vargas, K. / Yeliseyev, V. / Parsonnet, J. / Haggerty, T.D. / Wang, G. / Simpson, J.B. / Jariwala, P.B. / ...Authors: Zhang, J. / Walker, M.E. / Sanidad, K.Z. / Zhang, H. / Liang, Y. / Zhao, E. / Chacon-Vargas, K. / Yeliseyev, V. / Parsonnet, J. / Haggerty, T.D. / Wang, G. / Simpson, J.B. / Jariwala, P.B. / Beaty, V.V. / Yang, J. / Yang, H. / Panigrahy, A. / Minter, L.M. / Kim, D. / Gibbons, J.G. / Liu, L. / Li, Z. / Xiao, H. / Borlandelli, V. / Overkleeft, H.S. / Cloer, E.W. / Major, M.B. / Goldfarb, D. / Cai, Z. / Redinbo, M.R. / Zhang, G.
History
DepositionOct 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,77110
Polymers166,4102
Non-polymers1,3618
Water15,043835
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-33 kcal/mol
Surface area46570 Å2
Unit cell
Length a, b, c (Å)54.354, 161.142, 86.947
Angle α, β, γ (deg.)90.000, 107.332, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Beta-glucuronidase /


Mass: 83204.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Roseburia hominis (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 835 / 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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 12.5 mg/mL protein, 0.2 M lithium chloride, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.4→39.07 Å / Num. obs: 55112 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.0504 / Rpim(I) all: 0.03193 / Rrim(I) all: 0.0598 / Net I/σ(I): 18.68
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.1243 / Mean I/σ(I) obs: 8.37 / Num. unique obs: 5470 / CC1/2: 0.981 / CC star: 0.995 / Rpim(I) all: 0.0781 / Rrim(I) all: 0.147 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MVH
Resolution: 2.4→39.07 Å / SU ML: 0.2251 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.9284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1952 2013 3.66 %
Rwork0.1408 53050 -
obs0.1428 55063 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 88 835 11023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006610442
X-RAY DIFFRACTIONf_angle_d0.877814190
X-RAY DIFFRACTIONf_chiral_restr0.05311499
X-RAY DIFFRACTIONf_plane_restr0.00431855
X-RAY DIFFRACTIONf_dihedral_angle_d11.93551426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.460.25171490.16133790X-RAY DIFFRACTION98.75
2.46-2.530.22661420.15043720X-RAY DIFFRACTION98.62
2.53-2.60.22951350.15483818X-RAY DIFFRACTION98.8
2.6-2.680.23751410.15693760X-RAY DIFFRACTION98.68
2.68-2.780.26471430.16113772X-RAY DIFFRACTION99.04
2.78-2.890.23331430.15623781X-RAY DIFFRACTION98.59
2.89-3.020.20011470.16533805X-RAY DIFFRACTION98.9
3.02-3.180.21311470.15633761X-RAY DIFFRACTION99.34
3.18-3.380.20091360.14463805X-RAY DIFFRACTION98.57
3.38-3.640.18641420.13583781X-RAY DIFFRACTION98.94
3.64-4.010.15911430.12653781X-RAY DIFFRACTION99.37
4.01-4.590.16771480.11883855X-RAY DIFFRACTION99.45
4.59-5.780.16161470.11793799X-RAY DIFFRACTION99.42
5.78-39.070.17241500.14283822X-RAY DIFFRACTION98.22

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