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- PDB-6lel: Structure of E. coli beta-glucuronidase complex with C6-hexyl uro... -

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Basic information

Entry
Database: PDB / ID: 6lel
TitleStructure of E. coli beta-glucuronidase complex with C6-hexyl uronic isofagomine
ComponentsBeta-D-glucuronidase
KeywordsHYDROLASE / inhibitor / glycosidase / isofagomine
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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
Chem-E8X / Beta-glucuronidase / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.498 Å
AuthorsLin, H.-Y. / Kuo, Y.-H. / Lin, C.-H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2113-M-001-001 Taiwan
CitationJournal: Commun Biol / Year: 2021
Title: Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Authors: Lin, H.Y. / Chen, C.Y. / Lin, T.C. / Yeh, L.F. / Hsieh, W.C. / Gao, S. / Burnouf, P.A. / Chen, B.M. / Hsieh, T.J. / Dashnyam, P. / Kuo, Y.H. / Tu, Z. / Roffler, S.R. / Lin, C.H.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)137,8104
Polymers137,3202
Non-polymers4912
Water2,252125
1
A: Beta-D-glucuronidase
B: Beta-D-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)275,6218
Polymers274,6404
Non-polymers9814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14510 Å2
ΔGint-96 kcal/mol
Surface area81570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.781, 76.720, 124.888
Angle α, β, γ (deg.)90.000, 124.640, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 195 or resid 197...
21(chain B and (resid 0 through 206 or resid 209 through 597))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISGLNGLN(chain A and (resid 0 through 195 or resid 197...AA0 - 1951 - 196
12CYSCYSVALVAL(chain A and (resid 0 through 195 or resid 197...AA197 - 206198 - 207
13ASNASNASNASN(chain A and (resid 0 through 195 or resid 197...AA209210
14HISHISHISHIS(chain A and (resid 0 through 195 or resid 197...AA01
15TRPTRPPHEPHE(chain A and (resid 0 through 195 or resid 197...AA242 - 365243 - 366
16LYSLYSPROPRO(chain A and (resid 0 through 195 or resid 197...AA370 - 597371 - 598
21HISHISVALVAL(chain B and (resid 0 through 206 or resid 209 through 597))BB0 - 2061 - 207
22ASNASNPROPRO(chain B and (resid 0 through 206 or resid 209 through 597))BB209 - 597210 - 598

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Components

#1: Protein Beta-D-glucuronidase / Beta-glucuronidase / NLS-GFP-GUS


Mass: 68659.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: uidA, A9R57_02750, ACN68_26240, ACN81_11215, ACU57_22480, AM270_03870, AM464_25945, AUQ13_03930, BANRA_00079, BANRA_00563, BANRA_02251, BB545_08625, BET08_08370, BHS87_09195, BJJ90_13245, BK292_ ...Gene: uidA, A9R57_02750, ACN68_26240, ACN81_11215, ACU57_22480, AM270_03870, AM464_25945, AUQ13_03930, BANRA_00079, BANRA_00563, BANRA_02251, BB545_08625, BET08_08370, BHS87_09195, BJJ90_13245, BK292_18725, BOH76_23450, BON63_17270, BON69_09035, BON71_25965, BUE81_02440, BvCms2454_03287, BvCmsHHP019_03955, BvCmsKKP061_00687, BvCmsKSP011_01150, BvCmsKSP024_03693, BvCmsKSP026_03508, BvCmsKSP045_00685, BvCmsKSP067_00118, BvCmsNSP047_02620, BvCmsSINP012_02859, BvCmsSIP019_00145, BVL39_19890, BW690_15740, BZL31_05290, C4J69_24575, C5N07_00485, C7235_11830, C9200_15785, C9E25_02740, C9Z12_02165, CA593_19915, CI694_12700, COD46_02605, CV83915_04776, D2185_18760, D3821_14300, D3Y67_19800, D9D20_10680, D9I11_03210, D9K48_06425, DBQ99_12860, DNQ41_12380, DXT69_06115, DXT71_07500, E2119_03270, E5P28_03750, E5S47_08220, EAI46_18055, EAI52_05705, EC3234A_33c01180, EC3426_02616, EEP23_13620, EL75_2040, EL79_2080, EL80_2107, ELT20_01525, EPS71_15340, ERS085365_00730, ERS085416_00883, ERS139211_01060, ERS150873_00637, EXX24_04480, EXX78_14190, EYD11_10940, EYY78_00120, FAX15_15905, FV293_04650, NCTC11181_05093, NCTC13462_05935, NCTC8500_02703, NCTC9045_02849, NCTC9062_00385, NCTC9706_03872, PU06_11555, RG28_14030, RK56_009440, SAMEA3472044_02684, SAMEA3472047_01270, SAMEA3472080_01417, SAMEA3484427_00776, SAMEA3484429_00887, SAMEA3752553_00640, SAMEA3752559_02259, SAMEA3753097_02320, SK85_01835, WR15_14365
Production host: Escherichia coli (E. coli)
References: UniProt: W8SYR0, UniProt: P05804*PLUS, beta-glucuronidase
#2: Chemical ChemComp-E8X / (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid


Mass: 245.315 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5 and 21% PEG4K

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.498→30 Å / Num. obs: 43895 / % possible obs: 97.9 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.057 / Rrim(I) all: 0.111 / Χ2: 0.864 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.592.80.63840240.7190.4120.7630.82590.3
2.59-2.6930.57341890.7290.3660.6820.81594.1
2.69-2.823.40.53442980.7710.3340.6320.84196.7
2.82-2.963.70.48844040.8630.2890.5690.85498.7
2.96-3.1540.39244760.9210.2240.4530.88499.9
3.15-3.3940.23344440.9620.1330.2690.90399.9
3.39-3.7340.12344710.9850.0710.1430.89899.9
3.73-4.273.90.07244860.9930.0420.0831.00599.7
4.27-5.383.80.04645100.9940.0270.0530.85699.8
5.38-303.70.03345930.9980.020.0390.71299.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k46

3k46


Resolution: 2.498→29.495 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31
RfactorNum. reflection% reflection
Rfree0.2863 1911 5.13 %
Rwork0.2379 --
obs0.2404 37251 82.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.43 Å2 / Biso mean: 58.3257 Å2 / Biso min: 1.36 Å2
Refinement stepCycle: final / Resolution: 2.498→29.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9521 0 34 125 9680
Biso mean--32.27 33.9 -
Num. residues----1184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139806
X-RAY DIFFRACTIONf_angle_d1.63613329
X-RAY DIFFRACTIONf_chiral_restr0.0881418
X-RAY DIFFRACTIONf_plane_restr0.011730
X-RAY DIFFRACTIONf_dihedral_angle_d8.7225713
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5282X-RAY DIFFRACTION11.723TORSIONAL
12B5282X-RAY DIFFRACTION11.723TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4984-2.56090.2762500.317296132
2.5609-2.63010.3609750.3195133044
2.6301-2.70740.3491990.3061180260
2.7074-2.79480.38521160.2897219473
2.7948-2.89460.32131350.2828252383
2.8946-3.01040.32791450.2785267789
3.0104-3.14720.31641480.2782280092
3.1472-3.31290.32291550.2562285394
3.3129-3.52020.28671610.246294497
3.5202-3.79150.29141640.2266302299
3.7915-4.17210.28011630.2124302099
4.1721-4.77360.24731640.2044302399
4.7736-6.00580.26711650.22293062100
6.0058-29.4950.24511710.2111312999

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