[English] 日本語
Yorodumi
- PDB-6tr3: Ruminococcus gnavus GH29 fucosidase E1_10125 in complex with fucose -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tr3
TitleRuminococcus gnavus GH29 fucosidase E1_10125 in complex with fucose
ComponentsF5/8 type C domain-containing protein
KeywordsHYDROLASE / fucosidase / fucose / ruminococcus gnavus / GH29
Function / homology
Function and homology information


(Ara-f)3-Hyp beta-L-arabinobiosidase / alpha-L-fucosidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
CalX-like domain superfamily / Glycoside hydrolase, family 29 / Alpha-L-fucosidase / Alpha-L-fucosidase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
beta-L-fucopyranose / F5/8 type C domain-containing protein / Beta-L-arabinobiosidase
Similarity search - Component
Biological species[Ruminococcus] gnavus E1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOwen, C.D. / Wu, H. / Crost, E. / Colvile, A. / Juge, N. / Walsh, M.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M029042 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J004529/1 United Kingdom
CitationJournal: Cell.Mol.Life Sci. / Year: 2021
Title: Fucosidases from the human gut symbiont Ruminococcus gnavus.
Authors: Wu, H. / Rebello, O. / Crost, E.H. / Owen, C.D. / Walpole, S. / Bennati-Granier, C. / Ndeh, D. / Monaco, S. / Hicks, T. / Colvile, A. / Urbanowicz, P.A. / Walsh, M.A. / Angulo, J. / Spencer, D.I.R. / Juge, N.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: F5/8 type C domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0518
Polymers61,7091
Non-polymers3427
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-42 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.219, 48.643, 80.287
Angle α, β, γ (deg.)90.000, 115.020, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein F5/8 type C domain-containing protein


Mass: 61708.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) [Ruminococcus] gnavus E1 (bacteria) / References: UniProt: A0A2N5PIE7, UniProt: A0A6N3BKT0*PLUS
#2: Sugar ChemComp-FUL / beta-L-fucopyranose / beta-L-fucose / 6-deoxy-beta-L-galactopyranose / L-fucose / fucose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride, 25% PEG 3350, 0.1 M bis-tris pH 5.5 20mg/ml protein

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→63.94 Å / Num. obs: 55407 / % possible obs: 99.1 % / Redundancy: 3.1 % / Biso Wilson estimate: 19.629 Å2 / Rpim(I) all: 0.054 / Rrim(I) all: 0.096 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.7-1.732.91.1797227300.4090.71697.5
4.61-63.9318.1888229190.0270.04999.6

-
Processing

Software
NameVersionClassification
xia2data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUE

4oue


Resolution: 1.7→63.94 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.164 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1099 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.108
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2187 2806 5.1 %RANDOM
Rwork0.1822 ---
obs0.184 52597 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 83 Å2 / Biso mean: 25.309 Å2 / Biso min: 6.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.49 Å2
2---0.11 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.7→63.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3978 0 17 270 4265
Biso mean--19.65 25.97 -
Num. residues----505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0194105
X-RAY DIFFRACTIONr_bond_other_d0.0010.023609
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.8715625
X-RAY DIFFRACTIONr_angle_other_deg1.0622.9328460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495510
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.98926.154208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.23915712
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6341510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2579
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.322 213 -
Rwork0.309 3844 -
obs--97.83 %
Refinement TLS params.Method: refined / Origin x: -1.671 Å / Origin y: 4.674 Å / Origin z: 18.278 Å
111213212223313233
T0.0339 Å2-0.0041 Å2-0.0186 Å2-0.0636 Å20.0092 Å2--0.0632 Å2
L1.3294 °20.1147 °20.0396 °2-0.4923 °20.1842 °2--0.5527 °2
S0.0299 Å °0.0879 Å °0.0917 Å °0.0901 Å °-0.0408 Å °0.0535 Å °0.0449 Å °-0.0734 Å °0.0109 Å °

+
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