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- PDB-6jz3: b-glucuronidase from Ruminococcus gnavus in complex with uronic d... -

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Basic information

Entry
Database: PDB / ID: 6jz3
Titleb-glucuronidase from Ruminococcus gnavus in complex with uronic deoxynojirimycin
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / b-glucuronidase
Function / homology
Function and homology information


beta-glucuronidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily ...Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CN0 / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.502 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)107-2627-M-001-006 Taiwan
CitationJournal: J.Med.Chem. / Year: 2020
Title: Substituent Position of Iminocyclitols Determines the Potency and Selectivity for Gut Microbial Xenobiotic-Reactivating Enzymes.
Authors: Dashnyam, P. / Lin, H.Y. / Chen, C.Y. / Gao, S. / Yeh, L.F. / Hsieh, W.C. / Tu, Z. / Lin, C.H.
History
DepositionApr 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 27, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,0105
Polymers145,5382
Non-polymers4723
Water23,0231278
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-20 kcal/mol
Surface area41800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.501, 103.331, 112.213
Angle α, β, γ (deg.)90.000, 130.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1132-

HOH

21B-1113-

HOH

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Components

#1: Protein Beta-glucuronidase /


Mass: 72768.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: uidA / Production host: Escherichia coli (E. coli) / References: UniProt: Q6W7J7
#2: Chemical ChemComp-CN0 / (2~{S},3~{R},4~{R},5~{S})-3,4,5-tris(oxidanyl)piperidine-2-carboxylic acid


Mass: 177.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11NO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1278 / 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: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 70% MPD, 0.1 M HEPES, pH 7.5, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 221212 / % possible obs: 99.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Χ2: 0.926 / Net I/σ(I): 16.8 / Num. measured all: 1038215
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.554.20.49220460.8140.270.5610.76299.6
1.55-1.624.40.359219560.8890.1950.410.82799.7
1.62-1.694.40.262220750.9360.1420.2990.87499.7
1.69-1.784.50.183221290.970.0980.2080.95999.9
1.78-1.894.60.126220630.9860.0660.1421.028100
1.89-2.044.80.083221530.9940.0430.0941.08499.9
2.04-2.244.90.056221770.9970.0280.0630.93499.9
2.24-2.5650.05220930.9970.0240.0560.99899.8
2.56-3.2350.043222010.9980.0210.0480.93899.7
3.23-305.10.041223190.9970.020.0450.83199.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.502→28.384 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.58
RfactorNum. reflection% reflection
Rfree0.1694 2000 5 %
Rwork0.149 --
obs0.1492 217997 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.23 Å2 / Biso mean: 17.4136 Å2 / Biso min: 3.96 Å2
Refinement stepCycle: final / Resolution: 1.502→28.384 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9495 0 52 1278 10825
Biso mean--14.02 28.13 -
Num. residues----1159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0179748
X-RAY DIFFRACTIONf_angle_d1.64213221
X-RAY DIFFRACTIONf_chiral_restr0.1121369
X-RAY DIFFRACTIONf_plane_restr0.011711
X-RAY DIFFRACTIONf_dihedral_angle_d13.5333554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5021-1.53970.24291210.2171258580
1.5397-1.58130.2581410.20071502296
1.5813-1.62780.22241500.18091555299
1.6278-1.68030.22931330.171515593100
1.6803-1.74040.19821480.163115658100
1.7404-1.81010.18991420.158115742100
1.8101-1.89240.17031490.15415660100
1.8924-1.99220.20051430.152115735100
1.9922-2.1170.17911450.141415686100
2.117-2.28030.16551390.141415716100
2.2803-2.50970.16591480.144515704100
2.5097-2.87260.16831470.151415730100
2.8726-3.61790.1461420.13341567799

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