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- PDB-5z1a: The crystal structure of Bacteroides fragilis beta-glucuronidase ... -

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Basic information

Entry
Database: PDB / ID: 5z1a
TitleThe crystal structure of Bacteroides fragilis beta-glucuronidase in complex with uronic isofagomine
ComponentsPutative beta-galactosidase
KeywordsHYDROLASE / beta-glucuronidase / GH2
Function / homology
Function and homology information


beta-glucuronidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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 ...Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / 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-SJ5 / Beta-glucuronidase
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.859 Å
AuthorsDashnyam, P. / Lin, H.Y. / Lin, C.H.
CitationJournal: To Be Published
Title: Dissection of the substrate preference and structure of gut microbial-glucuronidases identifies the major bacteria causing xenobiotic toxicity
Authors: Dashnyam, P. / Mudududdla, R. / Hsieh, T.J. / Lin, T.C. / Lin, H.Y. / Chen, P.Y. / Hsu, C.Y. / Lin, C.H.
History
DepositionDec 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 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: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0542
Polymers77,8931
Non-polymers1611
Water15,025834
1
A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules

A: Putative beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)312,2158
Polymers311,5714
Non-polymers6454
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area12120 Å2
ΔGint-11 kcal/mol
Surface area91720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.253, 103.135, 199.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1039-

HOH

21A-1303-

HOH

31A-1490-

HOH

41A-1529-

HOH

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Components

#1: Protein Putative beta-galactosidase /


Mass: 77892.711 Da / Num. of mol.: 1 / Fragment: UNP residues 38-690
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: NCTC 9343 / Gene: BF9343_0320 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LIC7
#2: Chemical ChemComp-SJ5 / (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid


Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 834 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 250mM DL-Malic acid, pH 7.0, 20%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.859→30 Å / Num. obs: 68429 / % possible obs: 98.3 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.028 / Rrim(I) all: 0.057 / Χ2: 0.832 / Net I/σ(I): 14.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.86-1.933.80.39167040.9140.2220.4520.84697.2
1.93-24.10.27968360.960.1520.3190.80299.4
2-2.094.30.18168840.9820.0970.2060.83299.9
2.09-2.214.40.13468860.9890.070.1510.859100
2.21-2.344.30.10369010.9920.0550.1170.94399.8
2.34-2.524.50.07369220.9950.0380.0830.81899.9
2.52-2.784.40.05169290.9970.0270.0580.80599.8
2.78-3.184.30.03468780.9980.0180.0390.74598.9
3.18-43.80.02966370.9970.0170.0341.01994.3
4-303.80.02568520.9980.0150.0290.6694.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.859→29.399 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19
RfactorNum. reflection% reflection
Rfree0.1897 2000 2.99 %
Rwork0.1534 --
obs0.1545 66841 95.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.02 Å2 / Biso mean: 22.475 Å2 / Biso min: 3.31 Å2
Refinement stepCycle: final / Resolution: 1.859→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 11 834 6150
Biso mean--15.78 32.67 -
Num. residues----655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115479
X-RAY DIFFRACTIONf_angle_d1.2517435
X-RAY DIFFRACTIONf_chiral_restr0.06776
X-RAY DIFFRACTIONf_plane_restr0.007972
X-RAY DIFFRACTIONf_dihedral_angle_d13.2292022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8595-1.9060.22091110.21863615372676
1.906-1.95750.31861250.20994025415084
1.9575-2.01510.21211360.16974424456093
2.0151-2.08010.20761430.16124637478097
2.0801-2.15440.21051460.15934750489699
2.1544-2.24070.231490.164448044953100
2.2407-2.34260.22631470.175447664913100
2.3426-2.4660.17241470.153847944941100
2.466-2.62050.22861490.157548174966100
2.6205-2.82260.21061480.151648024950100
2.8226-3.10640.20111500.151848374987100
3.1064-3.55530.15021480.14274816496499
3.5553-4.47670.15561470.13224742488997
4.4767-29.40260.16591540.14425012516699

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