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- PDB-7byw: Crystal structure of Acidovorax avenae L-fucose mutarotase (L-fuc... -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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