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- PDB-4jhz: Structure of E. coli beta-Glucuronidase bound with a novel, poten... -

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Basic information

Entry
Database: PDB / ID: 4jhz
TitleStructure of E. coli beta-Glucuronidase bound with a novel, potent inhibitor 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide
ComponentsBeta-glucuronidase
Keywordshydrolase/hydrolase inhibitor / alpha/beta barrel / sugar-binding domain / beta-sandwich domain / hydrolase-hydrolase inhibitor complex
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 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-1KV / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.831 Å
AuthorsRoberts, A.B. / Wallace, B.D. / Redinbo, M.R.
CitationJournal: Mol.Pharmacol. / Year: 2013
Title: Molecular Insights into Microbial beta-Glucuronidase Inhibition to Abrogate CPT-11 Toxicity.
Authors: Roberts, A.B. / Wallace, B.D. / Venkatesh, M.K. / Mani, S. / Redinbo, M.R.
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 1.2Dec 6, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,0384
Polymers138,1992
Non-polymers8392
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-17 kcal/mol
Surface area43660 Å2
MethodPISA
2
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)278,0758
Polymers276,3974
Non-polymers1,6784
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_758-x+2,y,-z+31
Buried area13360 Å2
ΔGint-88 kcal/mol
Surface area80140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.305, 77.408, 126.291
Angle α, β, γ (deg.)90.00, 124.84, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 69099.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1617, gurA, gusA, JW1609, uidA / Production host: Escherichia coli (E. coli) / References: UniProt: P05804, beta-glucuronidase
#2: Chemical ChemComp-1KV / 2-[4-(1,3-benzodioxol-5-ylmethyl)piperazin-1-yl]-N-[(1S,2S,5S)-2,5-dimethoxycyclohexyl]acetamide


Mass: 419.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H33N3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.44 Å3/Da / Density % sol: 49.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 17% PEG 3350, 0.25 M MgAcetate, 0.02% sodium azide, 1mM 5,6-DIHYDRO-BENZO[H]CINNOLIN-3-YLAMINE, pH 7.4, vapor diffusion, hanging drop, temperature 289K, VAPOR DIFFUSION, HANGING DROP

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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: Jul 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.83→46.508 Å / Num. all: 31648 / Num. obs: 31648 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.83→2.92 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1299)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K46

3k46


Resolution: 2.831→46.508 Å / SU ML: 0.37 / σ(F): 1.42 / Phase error: 25.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1604 5.07 %
Rwork0.1957 --
obs0.1983 31634 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.831→46.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9429 0 60 124 9613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039747
X-RAY DIFFRACTIONf_angle_d0.90313287
X-RAY DIFFRACTIONf_dihedral_angle_d16.0733431
X-RAY DIFFRACTIONf_chiral_restr0.0351425
X-RAY DIFFRACTIONf_plane_restr0.0041731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8314-2.92270.3171520.26592659X-RAY DIFFRACTION97
2.9227-3.02720.26691450.24722692X-RAY DIFFRACTION99
3.0272-3.14840.32081470.24592707X-RAY DIFFRACTION99
3.1484-3.29160.2971420.23782731X-RAY DIFFRACTION99
3.2916-3.46510.28211460.2222706X-RAY DIFFRACTION99
3.4651-3.68210.25781380.21232741X-RAY DIFFRACTION99
3.6821-3.96630.24451470.19162697X-RAY DIFFRACTION99
3.9663-4.36520.2471450.17752756X-RAY DIFFRACTION99
4.3652-4.99620.19361540.15922748X-RAY DIFFRACTION99
4.9962-6.29220.2161470.18312767X-RAY DIFFRACTION99
6.2922-46.5140.24571410.17922826X-RAY DIFFRACTION99
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)
11.6571-0.3187-0.00790.74750.22010.96290.15321.6327-0.2819-0.2508-0.0947-0.3306-0.06010.4324-0.08050.39350.06310.16431.0852-0.21940.429388.2406-32.6325130.5286
24.286-2.1742.53474.1396-1.77085.56130.25620.3383-0.17130.11110.0484-0.40390.21530.2152-0.33360.2515-0.02130.05930.4409-0.09030.460996.6312-29.3316147.067
33.97630.2738-0.11461.14270.21681.37490.1713-0.31220.270.1119-0.0518-0.1042-0.14180.1138-0.08870.3179-0.02390.05030.19270.00540.258481.579-21.266155.8499
40.30260.0519-0.30250.14560.25951.9580.07541.103-0.0937-0.47980.00910.054-0.03050.12070.06210.56910.120.02942.0336-0.2237-0.320265.4978-29.9742115.7236
51.13941.01990.91651.1954-0.01283.24860.13580.4772-0.1667-0.16340.14620.071-0.1065-0.37030.24080.47680.0362-0.12451.2951-0.41120.417154.7316-36.5033119.8169
60.3064-0.1241-0.44810.59361.24522.9056-0.04940.1956-0.1536-0.4384-0.09490.05880.1608-0.0438-0.05390.77670.0889-0.02831.2812-1.06691.341368.6758-66.2329110.1368
70.4915-0.01970.13941.20160.52390.8769-0.1240.8172-0.6981-0.2644-0.12140.09150.0902-0.0755-0.09230.57360.0114-0.01130.956-1.02680.934462.6201-54.7213125.2905
81.0607-0.00290.38131.16630.78281.94440.09760.1152-0.0945-0.22470.0743-0.04880.0796-0.10870.21130.6097-0.047-0.12560.8875-0.67750.791654.7108-49.2379126.0809
90.48780.11490.14380.56870.15160.92990.09271.0564-1.3268-0.04760.10980.41220.2358-0.44240.2960.4282-0.14-0.19380.817-0.76521.307846.6881-53.8796134.5464
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 344 )
2X-RAY DIFFRACTION2chain 'A' and (resid 345 through 420 )
3X-RAY DIFFRACTION3chain 'A' and (resid 421 through 601 )
4X-RAY DIFFRACTION4chain 'B' and (resid -1 through 135 )
5X-RAY DIFFRACTION5chain 'B' and (resid 136 through 190 )
6X-RAY DIFFRACTION6chain 'B' and (resid 191 through 252 )
7X-RAY DIFFRACTION7chain 'B' and (resid 253 through 334 )
8X-RAY DIFFRACTION8chain 'B' and (resid 335 through 371 )
9X-RAY DIFFRACTION9chain 'B' and (resid 372 through 601 )

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