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- PDB-6mvf: Crystal structure of FMN-binding beta-glucuronidase from Facaelib... -

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Basic information

Entry
Database: PDB / ID: 6mvf
TitleCrystal structure of FMN-binding beta-glucuronidase from Facaelibacterium prausnitzii L2-6
ComponentsBeta-galactosidase/beta-glucuronidase
KeywordsHYDROLASE / glycoside hydrolase / FMN / beta-glucuronidase
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / cellulose catabolic process / nucleotide binding
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Beta-galactosidase/beta-glucuronidase
Similarity search - Component
Biological speciesFaecalibacterium prausnitzii L2-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPellock, S.J. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J. Mol. Biol. / Year: 2019
Title: Discovery and Characterization of FMN-Binding beta-Glucuronidases in the Human Gut Microbiome.
Authors: Pellock, S.J. / Walton, W.G. / Ervin, S.M. / Torres-Rivera, D. / Creekmore, B.C. / Bergan, G. / Dunn, Z.D. / Li, B. / Tripathy, A. / Redinbo, M.R.
History
DepositionOct 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-galactosidase/beta-glucuronidase
B: Beta-galactosidase/beta-glucuronidase
C: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
E: Beta-galactosidase/beta-glucuronidase
F: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,42712
Polymers517,6896
Non-polymers2,7386
Water25,1851398
1
A: Beta-galactosidase/beta-glucuronidase
C: Beta-galactosidase/beta-glucuronidase
F: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,2136
Polymers258,8443
Non-polymers1,3693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-35 kcal/mol
Surface area64660 Å2
MethodPISA
2
B: Beta-galactosidase/beta-glucuronidase
D: Beta-galactosidase/beta-glucuronidase
E: Beta-galactosidase/beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,2136
Polymers258,8443
Non-polymers1,3693
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9120 Å2
ΔGint-36 kcal/mol
Surface area64670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.556, 106.815, 183.823
Angle α, β, γ (deg.)90.00, 90.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-galactosidase/beta-glucuronidase


Mass: 86281.453 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii L2-6 (bacteria)
Gene: FP2_04120 / Production host: Escherichia coli (E. coli) / References: UniProt: D4K3H3, beta-galactosidase
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1398 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 11.1 mg/mL protein, 0.2 M magnesium chloride, 10% w/v PEG 3000, 0.1 M sodium cacodylate

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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 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→29.52 Å / Num. obs: 163078 / % possible obs: 99.58 % / Redundancy: 5 % / Rmerge(I) obs: 0.1212 / Net I/σ(I): 11.22
Reflection shellResolution: 2.55→2.641 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.5703 / Mean I/σ(I) obs: 2.58 / Num. unique obs: 16164 / % possible all: 99.53

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CMG

3cmg


Resolution: 2.55→29.524 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2261 2002 1.23 %
Rwork0.1673 --
obs0.168 162836 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→29.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30456 0 186 1398 32040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00831501
X-RAY DIFFRACTIONf_angle_d0.98142924
X-RAY DIFFRACTIONf_dihedral_angle_d15.09118330
X-RAY DIFFRACTIONf_chiral_restr0.0554596
X-RAY DIFFRACTIONf_plane_restr0.0065598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.61370.33271400.23511387X-RAY DIFFRACTION99
2.6137-2.68440.33171430.217911416X-RAY DIFFRACTION100
2.6844-2.76330.27851440.206911497X-RAY DIFFRACTION100
2.7633-2.85240.29481420.213611428X-RAY DIFFRACTION100
2.8524-2.95430.28781440.198511519X-RAY DIFFRACTION100
2.9543-3.07240.26721410.19311460X-RAY DIFFRACTION100
3.0724-3.21210.24211430.183811449X-RAY DIFFRACTION100
3.2121-3.38120.23531390.181911474X-RAY DIFFRACTION100
3.3812-3.59270.20811430.168411517X-RAY DIFFRACTION100
3.5927-3.86960.22681430.158811467X-RAY DIFFRACTION100
3.8696-4.2580.19941440.139711547X-RAY DIFFRACTION100
4.258-4.87170.15611460.119611518X-RAY DIFFRACTION100
4.8717-6.12880.19351440.14411580X-RAY DIFFRACTION100
6.1288-29.5260.20151460.15811575X-RAY DIFFRACTION98

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