5Z6B

Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of sugar-binding protein YesO in complex with rhamnogalacturonan trisaccharide

Sugiura, H.Oiki, S.Mikami, B.Murata, K.Hashimoto, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative ABC transporter substrate-binding protein YesOA427Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: yesOBSU06970
UniProt
Find proteins for O31518 (Bacillus subtilis (strain 168))
Explore O31518 
Go to UniProtKB:  O31518
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranoseB3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G48077ST
GlyCosmos:  G48077ST
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.23α = 90
b = 78.592β = 102.04
c = 54.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fuji Foundation for Protein ResearchJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary