[English] 日本語
Yorodumi
- PDB-6ed2: Faecalibacterium prausnitzii beta-glucuronidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ed2
TitleFaecalibacterium prausnitzii beta-glucuronidase
ComponentsGlycosyl hydrolase family 2, TIM barrel domain protein
KeywordsHYDROLASE / glycosyl hydrolase
Function / homology
Function and homology information


beta-galactosidase / beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
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 ...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
FORMIC ACID / Beta-galactosidase
Similarity search - Component
Biological speciesFaecalibacterium prausnitzii A2-165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPellock, S.J. / Biernat, K.A. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Sci Rep / Year: 2019
Title: Structure, function, and inhibition of drug reactivating human gut microbial beta-glucuronidases.
Authors: Biernat, K.A. / Pellock, S.J. / Bhatt, A.P. / Bivins, M.M. / Walton, W.G. / Tran, B.N.T. / Wei, L. / Snider, M.C. / Cesmat, A.P. / Tripathy, A. / Erie, D.A. / Redinbo, M.R.
History
DepositionAug 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3148
Polymers71,9891
Non-polymers3257
Water6,413356
1
A: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules

A: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules

A: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules

A: Glycosyl hydrolase family 2, TIM barrel domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,25532
Polymers287,9564
Non-polymers1,29928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area20310 Å2
ΔGint-163 kcal/mol
Surface area73100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.232, 145.232, 233.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-849-

HOH

21A-870-

HOH

31A-1057-

HOH

-
Components

#1: Protein Glycosyl hydrolase family 2, TIM barrel domain protein


Mass: 71988.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii A2-165 (bacteria)
Gene: FAEPRAA2165_01145 / Production host: Escherichia coli (E. coli) / References: UniProt: C7H4D2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.95 Å3/Da / Density % sol: 75.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-Tris Propane: HCl, pH 7 0.4 M Magnesium Formate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→28.85 Å / Num. obs: 67984 / % possible obs: 99.56 % / Redundancy: 9.1 % / Net I/σ(I): 19.48
Reflection shellResolution: 2.3→2.382 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→28.85 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.72
RfactorNum. reflection% reflection
Rfree0.1985 1998 3.07 %
Rwork0.1717 --
obs0.1726 65044 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 20 356 5146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084937
X-RAY DIFFRACTIONf_angle_d0.9066700
X-RAY DIFFRACTIONf_dihedral_angle_d7.5773973
X-RAY DIFFRACTIONf_chiral_restr0.054706
X-RAY DIFFRACTIONf_plane_restr0.006868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.35760.26751400.23084425X-RAY DIFFRACTION100
2.3576-2.42130.27591410.2214443X-RAY DIFFRACTION100
2.4213-2.49250.24041400.20484397X-RAY DIFFRACTION100
2.4925-2.57290.24071410.20034448X-RAY DIFFRACTION100
2.5729-2.66480.23641400.19124430X-RAY DIFFRACTION100
2.6648-2.77140.18841420.18844451X-RAY DIFFRACTION100
2.7714-2.89740.20681410.19294471X-RAY DIFFRACTION100
2.8974-3.050.18411410.18994467X-RAY DIFFRACTION100
3.05-3.24090.21971420.1794487X-RAY DIFFRACTION100
3.2409-3.49070.1981430.1714494X-RAY DIFFRACTION100
3.4907-3.84130.19191420.16094502X-RAY DIFFRACTION100
3.8413-4.39560.18621440.14244556X-RAY DIFFRACTION100
4.3956-5.53170.15791470.13574609X-RAY DIFFRACTION100
5.5317-29.16370.18361540.17634866X-RAY DIFFRACTION100

+
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