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), 0.253 (DCC)
R-Value Work:
0.199 (Depositor), 0.201 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 48.39 kDa
Atom Count: 3,145
Modeled Residue Count: 376
Deposited Residue Count: 427
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31518
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.258 (Depositor), 0.253 (DCC)
R-Value Work: 0.199 (Depositor), 0.201 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-23

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.