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- PDB-6lej: Structure of E. coli beta-glucuronidase complex with C6-propyl ur... -

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Basic information

Entry
Database: PDB / ID: 6lej
TitleStructure of E. coli beta-glucuronidase complex with C6-propyl uronic isofagomine
Components(Beta-D-glucuronidase) x 2
KeywordsHYDROLASE / inhibitor / glycosidase / isofagomine
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase activity / beta-glucuronidase / 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 / 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-CKX / Beta-glucuronidase / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.617 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)137,7324
Polymers137,3262
Non-polymers4062
Water1,17165
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)275,4648
Polymers274,6514
Non-polymers8134
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area15290 Å2
ΔGint-102 kcal/mol
Surface area81200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.686, 76.551, 125.426
Angle α, β, γ (deg.)90.000, 124.850, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 195 or resid 200 through 237 or resid 245 through 599))
21(chain B and resid 1 through 599)

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
11METMETGLNGLN(chain A and (resid 1 through 195 or resid 200 through 237 or resid 245 through 599))AA1 - 1954 - 198
12ALAALAVALVAL(chain A and (resid 1 through 195 or resid 200 through 237 or resid 245 through 599))AA200 - 237203 - 240
13GLYGLYGLNGLN(chain A and (resid 1 through 195 or resid 200 through 237 or resid 245 through 599))AA245 - 599248 - 602
21METMETGLNGLN(chain B and resid 1 through 599)BB1 - 5991 - 599

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Components

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


Mass: 68804.000 Da / Num. of mol.: 1
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: Protein Beta-D-glucuronidase / Beta-glucuronidase / NLS-GFP-GUS


Mass: 68521.727 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-CKX / (2~{S},3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)-2-propyl-piperidine-3-carboxylic acid


Mass: 203.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.41 Å3/Da / Density % sol: 48.86 %
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: 2.26→30 Å / Num. obs: 61283 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Rrim(I) all: 0.092 / Χ2: 0.897 / Net I/σ(I): 7.5 / Num. measured all: 325144
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.26-2.344.60.57355460.8380.2840.6420.72489.1
2.34-2.435.20.51461190.8940.2430.570.73298
2.43-2.555.70.41261530.9360.1880.4530.751100
2.55-2.685.80.32262520.9550.1450.3540.801100
2.68-2.855.80.22462410.9760.1020.2460.85899.9
2.85-3.075.80.15962290.9850.0730.1751.01399.9
3.07-3.375.60.10562690.990.0490.1161.14299.7
3.37-3.865.20.06862020.9940.0340.0761.19698.9
3.86-4.864.50.04759970.9950.0260.0541.0395.4
4.86-304.70.03662750.9970.0190.0410.66797.9

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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: 2.617→29.748 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.2
RfactorNum. reflection% reflection
Rfree0.2797 1999 6.32 %
Rwork0.2367 --
obs0.2394 31639 79.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.78 Å2 / Biso mean: 57.1598 Å2 / Biso min: 2.08 Å2
Refinement stepCycle: final / Resolution: 2.617→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9507 0 28 65 9600
Biso mean--36.81 36.94 -
Num. residues----1187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0129784
X-RAY DIFFRACTIONf_angle_d1.53113306
X-RAY DIFFRACTIONf_chiral_restr0.0851420
X-RAY DIFFRACTIONf_plane_restr0.011731
X-RAY DIFFRACTIONf_dihedral_angle_d8.3735698
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5261X-RAY DIFFRACTION13.68TORSIONAL
12B5261X-RAY DIFFRACTION13.68TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.617-2.68210.4672410.339259423
2.6821-2.75460.3851600.336890234
2.7546-2.83560.3725900.3244134251
2.8356-2.9270.33311160.3234171465
2.927-3.03160.32641300.3212193874
3.0316-3.15280.37741480.3019217682
3.1528-3.29610.33821610.2801238691
3.2961-3.46960.34341760.2662260599
3.4696-3.68670.26411790.24682666100
3.6867-3.97070.27891760.22372620100
3.9707-4.36920.2481790.20622644100
4.3692-4.99880.27671790.19882659100
4.9988-6.28820.24331800.22072661100
6.2882-29.7480.21311840.1932273399
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)
10.08060.21090.18910.56390.50950.46120.21160.853-0.4739-0.2293-0.1605-0.26490.20710.2689-0.05770.69230.24230.02631.2042-0.51510.9018-7.8956-47.494723.5919
20.4622-0.06140.18110.60580.18610.16550.13460.8078-0.1945-0.4563-0.095-0.28270.09370.3296-0.21590.46980.33090.10131.0173-0.46250.6236-4.7192-39.636727.3529
30.80350.3265-0.72021.6517-0.62881.33580.02811.08280.1992-0.6120.0203-0.326-0.1480.3827-0.0620.4387-0.02240.21810.97810.17770.3689-11.2415-18.11326.7772
40.5110.09810.72641.48391.09452.050.26340.1313-0.08430.10620.1546-0.44090.37350.272-0.31990.22680.07780.11810.5724-0.15180.3968-0.1027-30.15744.5807
50.1843-0.29140.20240.86180.08161.23760.1553-0.15580.43730.0485-0.0792-0.1679-0.18490.4868-0.06170.274-0.08410.0910.2205-0.00660.3097-10.7774-20.392154.2584
61.6796-0.1790.56590.75480.10941.63430.07540.20880.24090.11350.0422-0.2091-0.2270.0477-0.09160.20420.04110.09270.1402-0.00540.3097-22.0596-22.985547.192
70.56-0.0703-0.37340.15370.10780.2760.2120.8067-0.0752-0.5959-0.0357-0.18190.01250.0776-0.08280.61440.13130.0991.4776-0.19750.3016-30.1238-29.930411.9781
80.27140.4417-0.63381.0333-0.21333.51910.10050.3424-0.0253-0.2547-0.0623-0.0437-0.41540.3344-0.02360.45240.1886-0.07431.0531-0.32050.3405-40.9499-32.838716.8576
90.03420.0869-0.14090.85670.06420.6923-0.04650.6177-0.4774-0.64870.0527-0.07150.3940.0817-0.03010.77330.2105-0.20891.0172-0.95131.1313-30.6902-58.283914.9991
100.1116-0.0370.3090.27360.05960.97490.16940.4813-0.5806-0.19770.14140.05770.29980.00070.37840.6240.036-0.39270.809-0.6491.0426-53.2295-52.204223.6581
110.4092-0.1527-0.0930.0872-0.10360.63080.14090.1727-0.84990.10660.014-0.02670.590.01850.0170.4835-0.0209-0.25170.1668-0.27380.9833-42.8152-54.316841.0323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 45 )A-2 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 210 )A46 - 210
3X-RAY DIFFRACTION3chain 'A' and (resid 211 through 344 )A211 - 344
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 420 )A345 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 539 )A421 - 539
6X-RAY DIFFRACTION6chain 'A' and (resid 540 through 599 )A540 - 599
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 126 )B1 - 126
8X-RAY DIFFRACTION8chain 'B' and (resid 127 through 183 )B127 - 183
9X-RAY DIFFRACTION9chain 'B' and (resid 184 through 344 )B184 - 344
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 512 )B345 - 512
11X-RAY DIFFRACTION11chain 'B' and (resid 513 through 600 )B513 - 600

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