[English] 日本語
Yorodumi
- PDB-6ncz: Crystal structure of hybrid beta-glucuronidase/beta-galacturonida... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ncz
TitleCrystal structure of hybrid beta-glucuronidase/beta-galacturonidase from Fusicatenibacter saccharivorans bound to phenyl-thio-beta-D-glucuronide
ComponentsBeta-glucuronidase
KeywordsHYDROLASE / glycoside hydrolase family 2 / beta-glucuronidase / beta-galacturonidase
Function / homology
Function and homology information


beta-galactosidase / carbohydrate catabolic process / beta-galactosidase activity
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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, active site / Glycosyl hydrolases family 2 acid/base catalyst. / 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-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
phenyl 1-thio-beta-D-glucopyranosiduronic acid / beta-galactosidase
Similarity search - Component
Biological speciesFusicatenibacter saccharivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWalton, W.G. / Pellock, S.J. / Redinbo, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Biochemistry / Year: 2019
Title: Selecting a Single Stereocenter: The Molecular Nuances That Differentiate beta-Hexuronidases in the Human Gut Microbiome.
Authors: Pellock, S.J. / Walton, W.G. / Redinbo, M.R.
History
DepositionDec 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-glucuronidase
B: Beta-glucuronidase
C: Beta-glucuronidase
D: Beta-glucuronidase
E: Beta-glucuronidase
F: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,85418
Polymers427,5836
Non-polymers2,27012
Water31,8511768
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25600 Å2
ΔGint-58 kcal/mol
Surface area119450 Å2
2
A: Beta-glucuronidase
B: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6120 Å2
ΔGint-21 kcal/mol
Surface area41970 Å2
MethodPISA
3
C: Beta-glucuronidase
E: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-19 kcal/mol
Surface area42280 Å2
MethodPISA
4
D: Beta-glucuronidase
F: Beta-glucuronidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,2856
Polymers142,5282
Non-polymers7574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-20 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.134, 116.916, 117.604
Angle α, β, γ (deg.)60.32, 62.53, 87.09
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Beta-glucuronidase /


Mass: 71263.914 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusicatenibacter saccharivorans (bacteria)
Gene: uidA_2, ERS852406_01826 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A174EHD1, beta-glucuronidase
#2: Sugar
ChemComp-FYJ / phenyl 1-thio-beta-D-glucopyranosiduronic acid / phenyl 1-thio-beta-D-glucosiduronic acid / phenyl 1-thio-D-glucosiduronic acid / phenyl 1-thio-glucosiduronic acid


Type: D-saccharide / Mass: 286.301 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H14O6S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1768 / 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: 2.63 Å3/Da / Density % sol: 53.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium tartrate dibasic, 20% (w/v) PEG 3350 with 1 mM phenyl-thio-beta-D-glucuronide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.2→29.7 Å / Num. obs: 215731 / % possible obs: 97.4 % / Redundancy: 3.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.071 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.6 % / Rmerge(I) obs: 1.093 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 21435 / CC1/2: 0.498 / Rpim(I) all: 0.664 / % possible all: 96.8

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LPF

3lpf


Resolution: 2.2→29.67 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2185 2010 0.93 %
Rwork0.1806 --
obs0.181 215654 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28928 0 150 1768 30846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00829756
X-RAY DIFFRACTIONf_angle_d0.94340256
X-RAY DIFFRACTIONf_dihedral_angle_d7.47517810
X-RAY DIFFRACTIONf_chiral_restr0.0564280
X-RAY DIFFRACTIONf_plane_restr0.0055200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2550.32051680.306215157X-RAY DIFFRACTION97
2.255-2.31590.31491170.287715168X-RAY DIFFRACTION97
2.3159-2.38410.30271360.265815093X-RAY DIFFRACTION96
2.3841-2.4610.30651550.253715103X-RAY DIFFRACTION97
2.461-2.54890.27041330.235115236X-RAY DIFFRACTION97
2.5489-2.65090.30461320.21415256X-RAY DIFFRACTION97
2.6509-2.77150.23841670.207815249X-RAY DIFFRACTION98
2.7715-2.91740.25291430.205615243X-RAY DIFFRACTION97
2.9174-3.10010.28481440.193115342X-RAY DIFFRACTION98
3.1001-3.33910.21591450.182115317X-RAY DIFFRACTION98
3.3391-3.67460.19591430.16215322X-RAY DIFFRACTION98
3.6746-4.2050.17321430.134915376X-RAY DIFFRACTION98
4.205-5.2930.16781430.126215368X-RAY DIFFRACTION98
5.293-29.67260.14731410.155815414X-RAY DIFFRACTION98

+
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://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