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- PDB-6jz4: b-glucuronidase from Ruminococcus gnavus in complex with D-glucar... -

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Basic information

Entry
Database: PDB / ID: 6jz4
Titleb-glucuronidase from Ruminococcus gnavus in complex with D-glucaro-d-lactam
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
Similarity search - Function
Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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 ...Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / 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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-EVA / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.712 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 1.0Jun 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 1.2Mar 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)146,0385
Polymers145,5382
Non-polymers5003
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-17 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.210, 101.896, 111.299
Angle α, β, γ (deg.)90.000, 130.900, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1198-

HOH

21B-1025-

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-EVA / (2S,3R,4S,5R)-3,4,5-trihydroxy-6-oxopiperidine-2-carboxylic acid


Mass: 191.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.47 Å3/Da / Density % sol: 50.13 %
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: 1.71→30 Å / Num. obs: 178565 / % possible obs: 99 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Rrim(I) all: 0.07 / Χ2: 0.928 / Net I/σ(I): 13.9 / Num. measured all: 696402
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.71-1.774.20.69141650.7750.3870.7950.76697.9
1.77-1.844.50.516142810.8810.2810.590.80798.4
1.84-1.934.60.358143170.9330.190.4070.88498.6
1.93-2.034.70.232143610.9710.1210.2630.93398.9
2.03-2.154.90.155143800.9860.080.1750.98499.1
2.15-2.3250.113144400.9910.0570.1270.98899.3
2.32-2.555.10.085144830.9940.0430.0961.0199.5
2.55-2.925.10.068145190.9960.0340.0761.21599.7
2.92-3.6850.04145790.9980.020.0451.03399.6
3.68-305.10.026146590.9990.0120.0290.61199.3

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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: 1.712→28.501 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.54
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I_MINUS AND I_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2028 2653 1.49 %
Rwork0.1678 --
obs0.1683 144184 61.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.34 Å2 / Biso mean: 18.2172 Å2 / Biso min: 5.35 Å2
Refinement stepCycle: final / Resolution: 1.712→28.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9442 0 64 750 10256
Biso mean--14.59 24.49 -
Num. residues----1153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079746
X-RAY DIFFRACTIONf_angle_d1.07713218
X-RAY DIFFRACTIONf_chiral_restr0.0441368
X-RAY DIFFRACTIONf_plane_restr0.0051712
X-RAY DIFFRACTIONf_dihedral_angle_d14.6613556
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7124-1.74360.18660.2093390126
1.7436-1.77710.2566700.2086497433
1.7771-1.81340.2664870.2109602640
1.8134-1.85280.23891060.2132688446
1.8528-1.89590.23491030.2069731349
1.8959-1.94330.20841270.1977746950
1.9433-1.99580.21071030.189752450
1.9958-2.05450.21491130.184765551
2.0545-2.12080.2071150.18774352
2.1208-2.19660.19151200.1779801654
2.1966-2.28450.21711270.172840256
2.2845-2.38840.20341400.1711895560
2.3884-2.51430.20391530.1609989666
2.5143-2.67170.19521640.16771117475
2.6717-2.87780.20842010.16271292787
2.8778-3.16710.20192040.16661412495
3.1671-3.62460.18812220.15371430496
3.6246-4.56360.18672020.1421392093
4.5636-100.20852300.17361470599

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