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- PDB-6jz5: b-glucuronidase from Ruminococcus gnavus in complex with D-glucur... -

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Basic information

Entry
Database: PDB / ID: 6jz5
Titleb-glucuronidase from Ruminococcus gnavus in complex with D-glucuronic acid
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 domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranuronic acid / Beta-glucuronidase
Similarity search - Component
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 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 10, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 23, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _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 2.2Nov 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)140,4664
Polymers140,0782
Non-polymers3882
Water18,9161050
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-19 kcal/mol
Surface area41080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.549, 103.178, 112.460
Angle α, β, γ (deg.)90.000, 130.990, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1060-

HOH

21B-1105-

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: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1050 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
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 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.579→30 Å / Num. obs: 313298 / % possible obs: 99.6 % / Redundancy: 5 % / Biso Wilson estimate: 11.93 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.032 / Rrim(I) all: 0.075 / Χ2: 0.987 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.58-1.644.80.402188140.9020.1970.4490.59198.9
1.64-1.750.301190010.940.1450.3350.59599.9
1.7-1.7850.221191300.9640.1060.2460.66799.8
1.78-1.8750.168190030.980.080.1860.76399.8
1.87-1.995.10.135190680.9850.0630.1491.0699.8
1.99-2.145.10.095190690.9920.0440.1051.14899.8
2.14-2.365.10.078191280.9940.0360.0861.28699.9
2.36-2.75.10.066190860.9950.0310.0731.34499.8
2.7-3.44.90.055191520.9960.0260.0611.44899.6
3.4-304.70.039191510.9970.0190.0430.92698.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z19

5z19


Resolution: 1.58→29.687 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1704 3322 1.06 %
Rwork0.1541 309976 -
obs0.1543 313298 82.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.34 Å2 / Biso mean: 18.0625 Å2 / Biso min: 2.31 Å2
Refinement stepCycle: final / Resolution: 1.58→29.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9409 0 44 1050 10503
Biso mean--13.12 27.95 -
Num. residues----1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079703
X-RAY DIFFRACTIONf_angle_d1.07113154
X-RAY DIFFRACTIONf_chiral_restr0.0451362
X-RAY DIFFRACTIONf_plane_restr0.0051702
X-RAY DIFFRACTIONf_dihedral_angle_d15.2553539
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.58-1.60170.2557810.1918703245
1.6017-1.62560.2144870.1816806052
1.6256-1.6510.2444810.1793848754
1.651-1.6780.1871000.1737880856
1.678-1.7070.19221090.1665922559
1.707-1.7380.1882930.1648975762
1.738-1.77140.20741160.15691028766
1.7714-1.80760.20071190.15141112971
1.8076-1.84690.15671330.15341188676
1.8469-1.88980.17281330.15121271482
1.8898-1.93710.18551570.1541345786
1.9371-1.98950.17321450.15311420991
1.9895-2.0480.17091590.14891491696
2.048-2.11410.16661510.15141530698
2.1141-2.18960.17181790.15051552599
2.1896-2.27720.17141520.155315514100
2.2772-2.38080.24261640.151915488100
2.3808-2.50630.16341780.154915568100
2.5063-2.66320.19841610.161815599100
2.6632-2.86870.15371680.161315512100
2.8687-3.15710.17121690.15431549899
3.1571-3.61330.1551610.14041538699
3.6133-4.54970.11481660.13421521497
4.5497-29.6870.18191600.17361539998
Refinement TLS params.Method: refined / Origin x: 130.2167 Å / Origin y: -871.6029 Å / Origin z: 277.9736 Å
111213212223313233
T0.0299 Å20.006 Å20.0048 Å2-0.0222 Å20.0022 Å2--0.0265 Å2
L0.1791 °20.0224 °20.0788 °2-0.0856 °2-0.0241 °2--0.1442 °2
S0.0056 Å °0.0148 Å °0.0017 Å °-0.015 Å °-0.0018 Å °0.0113 Å °-0.0081 Å °-0.0074 Å °-0.0007 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 597
2X-RAY DIFFRACTION1allB2 - 597
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 1277
5X-RAY DIFFRACTION1allS1283 - 1296

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