[English] 日本語
Yorodumi
- PDB-5czk: Structure of E. coli beta-glucuronidase bound with a novel, poten... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5czk
TitleStructure of E. coli beta-glucuronidase bound with a novel, potent inhibitor 1-((6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea
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-57Z / Beta-glucuronidase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsRoberts, A.R. / Wallace, B.R. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA98468 United States
CitationJournal: Chem.Biol. / Year: 2015
Title: Structure and Inhibition of Microbiome beta-Glucuronidases Essential to the Alleviation of Cancer Drug Toxicity.
Authors: Wallace, B.D. / Roberts, A.B. / Pollet, R.M. / Ingle, J.D. / Biernat, K.A. / Pellock, S.J. / Venkatesh, M.K. / Guthrie, L. / O'Neal, S.K. / Robinson, S.J. / Dollinger, M. / Figueroa, E. / ...Authors: Wallace, B.D. / Roberts, A.B. / Pollet, R.M. / Ingle, J.D. / Biernat, K.A. / Pellock, S.J. / Venkatesh, M.K. / Guthrie, L. / O'Neal, S.K. / Robinson, S.J. / Dollinger, M. / Figueroa, E. / McShane, S.R. / Cohen, R.D. / Jin, J. / Frye, S.V. / Zamboni, W.C. / Pepe-Ranney, C. / Mani, S. / Kelly, L. / Redinbo, M.R.
History
DepositionJul 31, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)139,5084
Polymers138,7132
Non-polymers7952
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-14 kcal/mol
Surface area44520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)169.140, 76.098, 125.831
Angle α, β, γ (deg.)90.00, 125.30, 90.00
Int Tables number5
Space group name H-MC121

-
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: K12 / Gene: uidA, gurA, gusA, b1617, JW1609 / Production host: Escherichia coli (E. coli) / References: UniProt: P05804, beta-glucuronidase
#2: Chemical ChemComp-57Z / 1-[(6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl]-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea


Mass: 397.491 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C21H23N3O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15% PEG 3350, 0.2 M MgAcetate, 0.02% sodium azide, 1 mM 1-((6,8-dimethyl-2-oxo-1,2-dihydroquinolin-3-yl)methyl)-1-(2-hydroxyethyl)-3-(4-hydroxyphenyl)thiourea

-
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 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→42 Å / Num. obs: 51255 / % possible obs: 99 % / Redundancy: 5.1 % / Net I/σ(I): 12.28
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.3 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→42 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2558 2609 5.09 %Random selection
Rwork0.2003 ---
obs0.2032 51242 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.39→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9596 0 56 407 10059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069914
X-RAY DIFFRACTIONf_angle_d1.22313489
X-RAY DIFFRACTIONf_dihedral_angle_d14.8223533
X-RAY DIFFRACTIONf_chiral_restr0.0481425
X-RAY DIFFRACTIONf_plane_restr0.0061759
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.43560.33821080.26752106X-RAY DIFFRACTION82
2.4356-2.48240.32231420.26352532X-RAY DIFFRACTION100
2.4824-2.53310.30171460.24622603X-RAY DIFFRACTION100
2.5331-2.58820.35561690.25192529X-RAY DIFFRACTION100
2.5882-2.64840.35231320.25162567X-RAY DIFFRACTION100
2.6484-2.71460.33061340.25912580X-RAY DIFFRACTION100
2.7146-2.7880.31521250.24522562X-RAY DIFFRACTION100
2.788-2.870.29291270.23242568X-RAY DIFFRACTION100
2.87-2.96260.32331160.22822621X-RAY DIFFRACTION100
2.9626-3.06840.27781320.21882594X-RAY DIFFRACTION100
3.0684-3.19130.25721440.21422564X-RAY DIFFRACTION100
3.1913-3.33640.28051320.21682598X-RAY DIFFRACTION100
3.3364-3.51230.28521440.20772558X-RAY DIFFRACTION100
3.5123-3.73220.23241430.19242576X-RAY DIFFRACTION100
3.7322-4.02010.24911580.17412588X-RAY DIFFRACTION100
4.0201-4.42430.20061410.1642596X-RAY DIFFRACTION100
4.4243-5.06360.21081360.15862608X-RAY DIFFRACTION100
5.0636-6.3760.23541410.18852616X-RAY DIFFRACTION100
6.376-42.01230.20581390.18322667X-RAY DIFFRACTION100
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)
11.60090.33-0.75791.23610.13432.71840.00020.7593-0.5021-0.1144-0.0178-0.19510.24290.28820.03190.29250.1102-0.03610.6389-0.23970.4454-6.942-45.692428.2373
20.9184-0.1657-0.81731.09080.23892.63060.10370.95680.3524-0.29260.0597-0.1702-0.36090.3041-0.21370.3344-0.07840.00980.92440.22210.4606-6.4218-16.294622.4754
34.2087-0.1208-0.32070.89170.34431.63610.0130.02660.20110.0804-0.0008-0.1017-0.08220.1703-0.02190.2638-0.0286-0.05520.1750.02440.2579-11.8746-23.371147.6828
41.06680.7663-0.46511.07350.06552.78780.01421.13370.1896-0.24690.06380.2077-0.02-0.0477-0.04860.38740.0601-0.09381.10250.03920.2469-34.4439-29.793413.9571
50.0325-0.1425-0.06150.73990.38890.83780.04321.0221-0.7164-0.33490.0135-0.05360.38890.11920.02630.6044-0.0043-0.0981.2879-0.88560.8885-29.8766-59.10269.8841
61.08610.30980.48570.73390.15182.45330.02140.6835-0.7891-0.01240.04250.27590.2527-0.3568-0.03790.3447-0.063-0.12190.639-0.34780.6923-47.4943-52.428328.8203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:173 )A-1 - 173
2X-RAY DIFFRACTION2( CHAIN A AND RESID 174:307 )A174 - 307
3X-RAY DIFFRACTION3( CHAIN A AND RESID 308:601 )A308 - 601
4X-RAY DIFFRACTION4( CHAIN B AND RESID -1:173 )B-1 - 173
5X-RAY DIFFRACTION5( CHAIN B AND RESID 174:307 )B174 - 307
6X-RAY DIFFRACTION6( CHAIN B AND RESID 308:601 )B308 - 601

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more