5Z6B | pdb_00005z6b

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

• PDB DOI: https://doi.org/10.2210/pdb5Z6B/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-22 Released: 2019-01-23 
• Deposition Author(s): Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
• Funding Organization(s): Fuji Foundation for Protein Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 48.86 kDa 
• Atom Count: 3,315 
• Modeled Residue Count: 393 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ABC transporter substrate-binding protein YesO	A	427	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: yesO, BSU06970
UniProt
Find proteins for O31518 (Bacillus subtilis (strain 168)) Explore O31518  Go to UniProtKB:  O31518

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-[beta-D-galactopyranose-(1-4)]alpha-L-rhamnopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G48077ST GlyCosmos: G48077ST

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.23	α = 90
b = 78.592	β = 102.04
c = 54.075	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Sugiura, H., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Fuji Foundation for Protein Research	Japan	--

Revision History  

• 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
• Version 2.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary