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- PDB-6jz1: Apo structure of b-glucuronidase from Ruminococcus gnavus at 1.7 ... -

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Basic information

Entry
Database: PDB / ID: 6jz1
TitleApo structure of b-glucuronidase from Ruminococcus gnavus at 1.7 Angstrom resolution
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / b-glucuronidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space
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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological species[Ruminococcus] gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsDashnyam, P. / Lin, H.Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) 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 1.0Jun 3, 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 1.2Nov 22, 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

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Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,4325
Polymers140,0782
Non-polymers3553
Water17,204955
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,86510
Polymers280,1564
Non-polymers7096
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area17350 Å2
ΔGint-62 kcal/mol
Surface area73860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.008, 103.128, 112.617
Angle α, β, γ (deg.)90.000, 130.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1118-

HOH

21B-1125-

HOH

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Components

#1: Protein Beta-glucuronidase


Mass: 70038.883 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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 955 / 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: 2.55 Å3/Da / Density % sol: 51.79 %
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: Oct 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 144698 / % possible obs: 99.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.036 / Rrim(I) all: 0.072 / Χ2: 0.941 / Net I/σ(I): 9.9 / Num. measured all: 566535
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.793.70.564144230.7590.3320.6570.67399.5
1.79-1.863.80.433144900.8390.2540.5050.7699.5
1.86-1.953.80.318144270.9540.1860.370.90199.3
1.95-2.053.80.221144730.9480.1280.2561.02199.3
2.05-2.183.90.153144810.9740.0880.1771.02699.5
2.18-2.3540.114145130.9860.0650.1311.07799.6
2.35-2.584.10.081145310.9920.0460.0930.99899.8
2.58-2.964.10.061145610.9950.0340.071.0499.7
2.96-3.7340.047144600.9960.0270.0541.14598.5
3.73-1040.034143390.9970.020.0390.7397

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Processing

Software
NameVersionClassification
PHENIX19-1692refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z19

5z19


Resolution: 1.73→29.71 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.192 2004 -
Rwork0.116 --
obs0.308 142326 97.4 %
Displacement parametersBiso max: 113.62 Å2 / Biso mean: 23.4642 Å2 / Biso min: 7.17 Å2
Refinement stepCycle: LAST / Resolution: 1.73→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9494 0 24 955 10473
LS refinement shellResolution: 1.731→1.793 Å
RfactorNum. reflection% reflection
Rfree0.281 --
Rwork0.2241 --
obs-3898 86.68 %

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