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- PDB-7byu: Crystal structure of Acidovorax avenae L-fucose mutarotase (apo form) -

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Basic information

Entry
Database: PDB / ID: 7byu
TitleCrystal structure of Acidovorax avenae L-fucose mutarotase (apo 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 / L-rhamnose mutarotase
Function and homology information
Biological speciesAcidovorax avenae subsp. avenae ATCC 19860 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.206 Å
AuthorsWatanabe, Y. / Fukui, 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 1.3Nov 29, 2023Group: 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

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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)28,9176
Polymers28,2882
Non-polymers6294
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-1 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.465, 69.465, 69.200
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 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.41 Å3/Da / Density % sol: 63.9 %
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: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18794 / % possible obs: 99.7 % / Redundancy: 5.2 % / CC1/2: 0.996 / Rpim(I) all: 0.037 / Rrim(I) all: 0.085 / Rsym value: 0.076 / Net I/σ(I): 10.6
Reflection shellResolution: 2.21→2.27 Å / Redundancy: 2.58 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1637 / CC1/2: 0.756 / Rpim(I) all: 0.372 / Rrim(I) all: 0.843 / Rsym value: 0.755 / % possible all: 98

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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: 1X8D

1x8d


Resolution: 2.206→45.415 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 29.59
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2398 1001 5.33 %
Rwork0.2169 --
obs0.2181 18763 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.5 Å2 / Biso mean: 61.1032 Å2 / Biso min: 31.79 Å2
Refinement stepCycle: final / Resolution: 2.206→45.415 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 42 62 1902
Biso mean--74.05 58.38 -
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 (%)
2.2062-2.32260.39011150.3227256799
2.3226-2.46810.32282060.29562473100
2.4681-2.65860.3051260.25542564100
2.6586-2.92610.3191410.28442526100
2.9261-3.34940.32771180.26182558100
3.3494-4.21940.24371460.20142536100
4.2194-45.4150.1671490.16952538100

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