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- PDB-6mvg: Crystal structure of FMN-binding beta-glucuronidase from Ruminoco... -

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Basic information

Entry
Database: PDB / ID: 6mvg
TitleCrystal structure of FMN-binding beta-glucuronidase from Ruminococcus gnavus
Componentsbeta-glucuronidase
KeywordsHYDROLASE / glycoside hydrolase / beta-glucuronidase / flavin-binding
Function / homologyGalactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta / FLAVIN MONONUCLEOTIDE
Function and homology information
Biological species[Ruminococcus] gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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-glucuronidase
B: beta-glucuronidase
C: beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,4129
Polymers265,9233
Non-polymers1,4896
Water1,874104
1
A: beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1373
Polymers88,6411
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1373
Polymers88,6411
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,1373
Polymers88,6411
Non-polymers4962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)236.028, 127.078, 88.819
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein beta-glucuronidase


Mass: 88640.859 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Ruminococcus] gnavus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20.4 mg/mL protein, 0.13 M magnesium acetate, 10% PEG 8000

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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: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→29.9 Å / Num. obs: 63747 / % possible obs: 99.74 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.07687 / Net I/σ(I): 14.03
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.6069 / Mean I/σ(I) obs: 2.36 / Num. unique obs: 6333 / % possible all: 99.91

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 2.8→29.876 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.77
RfactorNum. reflection% reflection
Rfree0.2456 2000 3.14 %
Rwork0.1854 --
obs0.1873 63726 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15460 0 96 104 15660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915985
X-RAY DIFFRACTIONf_angle_d1.07221708
X-RAY DIFFRACTIONf_dihedral_angle_d16.6819270
X-RAY DIFFRACTIONf_chiral_restr0.0582225
X-RAY DIFFRACTIONf_plane_restr0.0062832
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.40951420.32574387X-RAY DIFFRACTION100
2.87-2.94750.38011410.28144376X-RAY DIFFRACTION100
2.9475-3.03420.30851440.25784407X-RAY DIFFRACTION100
3.0342-3.1320.34091410.2544365X-RAY DIFFRACTION100
3.132-3.24380.28841430.24334405X-RAY DIFFRACTION100
3.2438-3.37350.28931430.22134402X-RAY DIFFRACTION100
3.3735-3.52680.29011440.20364435X-RAY DIFFRACTION100
3.5268-3.71240.25041410.19034371X-RAY DIFFRACTION100
3.7124-3.94460.26791420.17864393X-RAY DIFFRACTION100
3.9446-4.24830.20791430.16034407X-RAY DIFFRACTION100
4.2483-4.67440.21321430.14574414X-RAY DIFFRACTION100
4.6744-5.34740.18121440.14054439X-RAY DIFFRACTION100
5.3474-6.72450.2071430.16454431X-RAY DIFFRACTION100
6.7245-29.87750.21431460.16664494X-RAY DIFFRACTION100

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