[English] 日本語
Yorodumi
- PDB-7byw: Crystal structure of Acidovorax avenae L-fucose mutarotase (L-fuc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7byw
TitleCrystal structure of Acidovorax avenae L-fucose mutarotase (L-fucose-bound form)
ComponentsL-fucose mutarotase
KeywordsSUGAR BINDING PROTEIN / L-fucose / Mutarotase
Function / homologyRhamnose/fucose mutarotase / L-rhamnose mutarotase / racemase and epimerase activity, acting on carbohydrates and derivatives / Dimeric alpha-beta barrel / Chem-1PG / alpha-L-fucopyranose / L-rhamnose mutarotase
Function and homology information
Biological speciesAcidovorax avenae subsp. avenae ATCC 19860 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsWatanabe, Y. / Watanabe, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Functional and structural characterization of a novel L-fucose mutarotase involved in non-phosphorylative pathway of L-fucose metabolism.
Authors: Watanabe, Y. / Watanabe, S. / Fukui, Y. / Nishiwaki, H.
History
DepositionApr 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Jun 24, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 29, 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: L-fucose mutarotase
B: L-fucose mutarotase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1216
Polymers28,2882
Non-polymers8334
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-5 kcal/mol
Surface area10610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.398, 68.398, 69.102
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

-
Components

#1: Protein L-fucose mutarotase


Mass: 14143.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acidovorax avenae subsp. avenae ATCC 19860 (bacteria)
Strain: ATCC 19860 / DSM 7227 / JCM 20985 / NCPPB 1011 / Gene: Acav_1655 / Production host: Escherichia coli (E. coli) / References: UniProt: F0Q4R9
#2: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#3: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 3.3 Å3/Da / Density % sol: 62.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 M potassium sodium tartrate, 0.1 M Tris-HCl pH 8.5, 0.5% PEGMME 5000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 36466 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.999 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Rsym value: 0.062 / Net I/σ(I): 17.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1945 / CC1/2: 0.634 / Rpim(I) all: 0.411 / Rrim(I) all: 1.285 / Rsym value: 1.216 / % possible all: 97.8

-
Processing

Software
NameVersionClassification
XDSdata processing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BYU

7byu


Resolution: 1.75→44.9876 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 30.51
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2466 1825 5.01 %
Rwork0.2262 --
obs0.2273 36430 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 41.1657 Å2 / Biso min: 21.02 Å2
Refinement stepCycle: final / Resolution: 1.75→44.9876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 56 153 2007
Biso mean--48.77 46.27 -
Num. residues----216
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.75-1.79730.35661340.3508266299
1.7973-1.85020.36861520.32052650100
1.8502-1.90990.35381270.28522681100
1.9099-1.97820.31631320.28312663100
1.9782-2.05740.28841280.26682667100
2.0574-2.1510.30431140.27392696100
2.151-2.26440.37941180.28612673100
2.2644-2.40630.28752100.2662594100
2.4063-2.59210.2941260.26582692100
2.5921-2.85290.32821440.26842682100
2.8529-3.26560.26751430.23672647100
3.2656-4.11390.21911420.19082653100
4.1139-44.98760.16911550.1752645100

+
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