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- PDB-3lpf: Structure of E. coli beta-Glucuronidase bound with a novel, poten... -

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Basic information

Entry
Database: PDB / ID: 3lpf
TitleStructure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 1-((6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea
ComponentsBeta-glucuronidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / alpha/beta barrel / sugar-binding domain / beta-sandwich domain / glycosyl hydrolase / beta-glucuronidase inhibitor / Glycosidase / Hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
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 / 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 domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-Z77 / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsWallace, B.D. / Redinbo, M.R.
CitationJournal: Science / Year: 2010
Title: Alleviating cancer drug toxicity by inhibiting a bacterial enzyme.
Authors: Wallace, B.D. / Wang, H. / Lane, K.T. / Scott, J.E. / Orans, J. / Koo, J.S. / Venkatesh, M. / Jobin, C. / Yeh, L.A. / Mani, S. / Redinbo, M.R.
History
DepositionFeb 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,5364
Polymers138,7132
Non-polymers8232
Water7,170398
1
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)279,0728
Polymers277,4264
Non-polymers1,6464
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15230 Å2
ΔGint-84 kcal/mol
Surface area82490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.058, 77.409, 126.152
Angle α, β, γ (deg.)90.000, 124.660, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-glucuronidase / / GUS / Beta-D-glucuronoside glucuronosohydrolase


Mass: 69356.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 / Gene: b1617, gurA, gusA, JW1609, uidA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P05804, beta-glucuronidase
#2: Chemical ChemComp-Z77 / 1-[(6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl]-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea


Mass: 411.517 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25N3O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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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: 49.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% PEG 3350, 0.2 M MgAcetate, 0.02% sodium azide, 1mM 1-((6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea, pH 7.4, vapor diffusion, ...Details: 15% PEG 3350, 0.2 M MgAcetate, 0.02% sodium azide, 1mM 1-((6,7-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(3-methoxyphenyl)thiourea, pH 7.4, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 59357 / % possible obs: 96.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.128 / Χ2: 62.14 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.3450.46523981.8378.9
2.34-2.385.30.43825321.68883.1
2.38-2.435.50.4226571.76287.3
2.43-2.485.70.427801.91492.7
2.48-2.535.90.36329862.01196.3
2.53-2.596.20.33930112.19599.3
2.59-2.666.50.32530382.31699.9
2.66-2.736.80.28530492.467100
2.73-2.816.90.25430553.078100
2.81-2.970.22230643.833100
2.9-37.10.20330574.607100
3-3.127.10.18130736.003100
3.12-3.267.20.16330187.392100
3.26-3.447.30.155307910.041100
3.44-3.657.40.142304912.156100
3.65-3.937.50.136307214.724100
3.93-4.337.60.121309116.303100
4.33-4.957.60.107309014.914100
4.95-6.247.60.094310812.108100
6.24-507.30.09531500.07999.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K4D

3k4d


Resolution: 2.26→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.8 / SU B: 18.674 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2908 4.9 %RANDOM
Rwork0.209 ---
obs0.211 59262 94.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 298.35 Å2 / Biso mean: 71.303 Å2 / Biso min: 10.24 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å2-0.16 Å2
2--1.59 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.26→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9644 0 58 398 10100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229966
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.92613564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.65551204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83924.297512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.389151566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9551558
X-RAY DIFFRACTIONr_chiral_restr0.1380.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217822
X-RAY DIFFRACTIONr_mcbond_it2.4591.55984
X-RAY DIFFRACTIONr_mcangle_it4.51729646
X-RAY DIFFRACTIONr_scbond_it3.49733982
X-RAY DIFFRACTIONr_scangle_it5.8694.53918
X-RAY DIFFRACTIONr_rigid_bond_restr2.18239966

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