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- PDB-6lem: Structure of E. coli beta-glucuronidase complex with C6-nonyl uro... -

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Basic information

Entry
Database: PDB / ID: 6lem
TitleStructure of E. coli beta-glucuronidase complex with C6-nonyl uronic isofagomine
Components(Beta-D-glucuronidase) x 2
KeywordsHYDROLASE / inhibitor / isofagomine / glycosidase
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-E9O / Beta-glucuronidase / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.188 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,5994
Polymers137,0242
Non-polymers5752
Water00
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)275,1988
Polymers274,0494
Non-polymers1,1504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13650 Å2
ΔGint-79 kcal/mol
Surface area84390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.361, 76.404, 126.400
Angle α, β, γ (deg.)90.000, 124.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 68746.953 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: 68277.375 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-E9O / (2~{S},3~{S},4~{R},5~{R})-2-nonyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid


Mass: 287.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H29NO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.43 Å3/Da / Density % sol: 49.4 %
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: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.188→30 Å / Num. obs: 21727 / % possible obs: 98.4 % / Redundancy: 6 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.069 / Rrim(I) all: 0.172 / Χ2: 0.817 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.312.90.79420030.5440.5130.9530.65991.2
3.31-3.453.90.70620880.8820.3920.8120.86295.8
3.45-3.65.10.53621760.9820.2650.6010.85199.4
3.6-3.796.20.4721780.9510.2060.5141.07699.7
3.79-4.036.60.33322090.9540.1410.3621.0299.9
4.03-4.347.20.17721770.9790.0710.1910.72499.9
4.34-4.787.30.12722030.9850.050.1370.724100
4.78-5.467.30.10422130.9870.0410.1120.78399.5
5.46-6.877.20.09222060.9890.0370.0990.73399.6
6.87-306.10.0422740.9970.0180.0440.71299.5

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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: 3.188→28.251 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.42
RfactorNum. reflection% reflection
Rfree0.2696 1856 9.8 %
Rwork0.2109 --
obs0.2167 18937 85.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 174.56 Å2 / Biso mean: 77.7292 Å2 / Biso min: 28.04 Å2
Refinement stepCycle: final / Resolution: 3.188→28.251 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9446 0 40 0 9486
Biso mean--71.97 --
Num. residues----1178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039732
X-RAY DIFFRACTIONf_angle_d0.66213227
X-RAY DIFFRACTIONf_chiral_restr0.0481409
X-RAY DIFFRACTIONf_plane_restr0.0041718
X-RAY DIFFRACTIONf_dihedral_angle_d6.6055675
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1883-3.27440.3793590.299654336
3.2744-3.37060.3641980.298491160
3.3706-3.47920.33961150.285109071
3.4792-3.60330.2881380.2633134288
3.6033-3.74720.36871360.2695124082
3.7472-3.91740.27831520.2276139492
3.9174-4.12330.26331590.1975141693
4.1233-4.38080.25011630.1906149897
4.3808-4.71760.25141660.1732151898
4.7176-5.18970.2331650.1755150099
5.1897-5.93460.26921670.1954152698
5.9346-7.45410.27761670.2256152398
7.4541-28.2510.22841710.1885158099
Refinement TLS params.Method: refined / Origin x: -11.8394 Å / Origin y: 1.105 Å / Origin z: 22.7773 Å
111213212223313233
T0.6677 Å2-0.0834 Å20.0552 Å2-0.5902 Å20.2526 Å2--0.5335 Å2
L1.9888 °20.0801 °20.162 °2-0.7052 °2-0.1292 °2--0.5876 °2
S0.1683 Å °-1.0018 Å °-0.5223 Å °0.2019 Å °-0.0825 Å °0.0114 Å °0.1081 Å °-0.1161 Å °-0.0961 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 601
2X-RAY DIFFRACTION1allB3 - 600
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allC2

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