5Z6C | pdb_00005z6c

Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan

• PDB DOI: https://doi.org/10.2210/pdb5Z6C/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

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus subtilis sugar-binding protein YesO involved in import of rhamnogalacturonan

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: 48.39 kDa 
• Atom Count: 3,145 
• Modelled Residue Count: 376 
• 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.258 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.184	α = 90
b = 108.578	β = 101.58
c = 40.494	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.

---

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

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description