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- PDB-6leg: Structure of E. coli beta-glucuronidase complex with uronic isofa... -

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Basic information

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


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / protein-containing complex / extracellular space / 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 / 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 ...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 / 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
Chem-SJ5 / Beta-glucuronidase / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 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 / pdbx_initial_refinement_model

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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
C: Beta-D-glucuronidase
D: Beta-D-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)275,2848
Polymers274,6404
Non-polymers6454
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-92 kcal/mol
Surface area81270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.527, 75.926, 168.281
Angle α, β, γ (deg.)90.000, 96.790, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-876-

HOH

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Components

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


Mass: 68659.875 Da / Num. of mol.: 4
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-SJ5 / (3S,4R,5R)-4,5-dihydroxypiperidine-3-carboxylic acid


Mass: 161.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 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: 2.6→30 Å / Num. obs: 79253 / % possible obs: 99.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.08 / Rrim(I) all: 0.179 / Χ2: 0.884 / Net I/σ(I): 6.4 / Num. measured all: 362631
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.692.90.7674890.7910.4680.8970.82594.7
2.69-2.83.40.85578760.8590.4790.9850.87199
2.8-2.934.10.94678810.8660.481.0660.86199.7
2.93-3.084.70.71779370.9310.3450.7990.88999.8
3.08-3.285.10.47879640.9590.2250.530.90799.8
3.28-3.535.20.26879450.9830.1270.2980.93899.8
3.53-3.885.20.14679650.9920.070.1620.93799.9
3.88-4.445.20.08180360.9950.040.090.93999.9
4.44-5.595.20.05280210.9960.0260.0590.83199.8
5.59-304.60.03781390.9980.0210.0430.78299

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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: 2.603→29.792 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 33.55
RfactorNum. reflection% reflection
Rfree0.2879 1873 2.8 %
Rwork0.2317 --
obs0.2333 66958 83.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.98 Å2 / Biso mean: 51.2965 Å2 / Biso min: 9.99 Å2
Refinement stepCycle: final / Resolution: 2.603→29.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19223 0 44 231 19498
Biso mean--30.99 36.28 -
Num. residues----2397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00819768
X-RAY DIFFRACTIONf_angle_d1.02926894
X-RAY DIFFRACTIONf_chiral_restr0.0582855
X-RAY DIFFRACTIONf_plane_restr0.0073507
X-RAY DIFFRACTIONf_dihedral_angle_d5.95911509
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6034-2.67380.3856720.31260944
2.6738-2.75240.3573910.3096322354
2.7524-2.84120.39061130.303370963
2.8412-2.94270.35781210.312424171
2.9427-3.06040.35811390.2945494483
3.0604-3.19950.361530.2829542091
3.1995-3.3680.35021630.2645559694
3.368-3.57860.29971650.2331574296
3.5786-3.85440.25841680.2192583498
3.8544-4.24130.24941700.2004587898
4.2413-4.85280.25021710.1953593199
4.8528-6.10530.28021730.2127597999
6.1053-29.7920.23261740.2013597997
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.12150.0339-0.29291.08060.04312.2688-0.10280.5095-0.2465-0.2671-0.06560.37690.0591-0.74280.08350.3142-0.0643-0.09490.5621-0.13690.338624.66356.25199.2848
22.54260.1108-1.31270.05530.27943.0078-0.14770.4545-0.2406-0.1029-0.02250.05880.0214-0.1470.12680.40740.0083-0.07550.1537-0.01580.306643.255713.295210.0831
33.03660.0215-0.35471.3948-0.42383.3312-0.0809-0.14690.25620.01990.0628-0.0927-0.53550.16110.02030.347-0.0221-0.05630.11580.00260.214950.024418.291326.4982
41.6512-1.06360.15851.5406-0.20942.9827-0.2326-0.5927-0.36310.40120.2739-0.16240.45060.7520.03620.60820.2924-0.00540.77690.20550.468570.1463-8.038173.2938
51.80380.0409-0.50980.87480.58942.3041-0.184-0.6701-0.1960.2930.1381-0.11290.17230.59730.01890.50690.25410.01190.67280.11980.292363.92133.044476.3865
62.7432-0.6665-0.12971.9438-0.53741.8841-0.1269-0.84940.33980.30130.0135-0.4722-0.18940.71190.12570.4931-0.0003-0.10480.7357-0.03760.281271.291222.50472.8864
72.4212-0.527-1.53291.1356-0.59655.4165-0.3261-0.5024-0.37260.20920.0264-0.03430.25140.29870.20430.4150.1181-0.0160.3056-0.02630.256454.00249.352768.143
83.13970.28191.00541.03550.14383.7568-0.1434-0.54020.24290.3484-0.07450.1505-0.3238-0.21440.15730.42890.05170.01840.2296-0.01370.270244.151716.836169.5145
93.40311.3066-0.3120.64380.00574.4224-0.1245-0.01510.2724-0.34480.13620.3723-0.34770.2714-0.05040.22520.0191-0.03260.24520.02430.211249.461216.154855.892
103.974-0.62480.35432.1561-1.71813.6588-0.10930.1472-0.00330.1660.04540.4697-0.2648-1.00680.04230.23490.05650.02870.4712-0.08940.4419.73159.662635.4314
110.9796-0.18370.96992.8133-0.08911.85020.00940.0786-0.6605-0.2686-0.0260.75350.7753-0.8886-0.09890.6769-0.33830.1190.8224-0.1690.89145.6443-19.739930.1088
121.4446-0.0135-0.74651.84020.01011.6167-0.2704-0.0079-0.52810.2942-0.06490.31940.44-0.70660.23430.5973-0.1510.12280.3612-0.03070.576918.6279-8.646943.9465
132.22880.10030.04831.4241-0.01332.1966-0.2999-0.2625-0.75480.26920.04360.21380.7773-0.36780.06190.5969-0.12910.15760.25270.02930.622724.0936-15.248751.4978
144.28990.2895-0.27582.84581.51243.69640.0077-0.4693-0.05460.01230.0824-0.385-0.06050.98760.01130.23750.0206-0.00590.57910.03280.262683.80558.070947.9154
151.43120.0282-0.39791.43880.49511.3394-0.208-0.2371-0.5060.09340.2452-0.18060.56620.8144-0.04380.60520.44990.10010.59620.12580.548781.4339-16.277841.5677
162.7881-1.0328-0.00451.5251-0.73361.5714-0.17340.1256-0.6932-0.1797-0.07560.17160.74060.20520.17230.6240.1310.07730.2458-0.0010.447259.5945-16.558632.8553
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 307 )A0 - 307
2X-RAY DIFFRACTION2chain 'A' and (resid 308 through 477 )A308 - 477
3X-RAY DIFFRACTION3chain 'A' and (resid 478 through 601 )A478 - 601
4X-RAY DIFFRACTION4chain 'B' and (resid 0 through 121 )B0 - 121
5X-RAY DIFFRACTION5chain 'B' and (resid 122 through 207 )B122 - 207
6X-RAY DIFFRACTION6chain 'B' and (resid 208 through 307 )B208 - 307
7X-RAY DIFFRACTION7chain 'B' and (resid 308 through 381 )B308 - 381
8X-RAY DIFFRACTION8chain 'B' and (resid 382 through 539 )B382 - 539
9X-RAY DIFFRACTION9chain 'B' and (resid 540 through 601 )B540 - 601
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 173 )C0 - 173
11X-RAY DIFFRACTION11chain 'C' and (resid 174 through 307 )C174 - 307
12X-RAY DIFFRACTION12chain 'C' and (resid 308 through 381 )C308 - 381
13X-RAY DIFFRACTION13chain 'C' and (resid 382 through 601 )C382 - 601
14X-RAY DIFFRACTION14chain 'D' and (resid 0 through 173 )D0 - 173
15X-RAY DIFFRACTION15chain 'D' and (resid 174 through 477 )D174 - 477
16X-RAY DIFFRACTION16chain 'D' and (resid 478 through 597 )D478 - 597

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