7E7M | pdb_00007e7m

Crystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB

• PDB DOI: https://doi.org/10.2210/pdb7E7M/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Streptococcus agalactiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-02-26 Released: 2022-03-02 
• Deposition Author(s): Pan, L.X., Wang, B., Yang, L.Y., Yang, D.F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure Analysis of the Streptococcus agalactiae Ribose Binding Protein RbsB

Pan, L.X., Wang, B., Yang, L.Y., Yang, D.F.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 137.1 kDa 
• Atom Count: 8,361 
• Modeled Residue Count: 1,120 
• Deposited Residue Count: 1,288 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ribose ABC transporter substrate-binding protein	A, B, C, D	322	Streptococcus agalactiae	Mutation(s): 0  Gene Names: rbsB
UniProt
Find proteins for Q8E283 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8E283  Go to UniProtKB:  Q8E283

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIP (Subject of Investigation/LOI)	E [auth A], F [auth B], G [auth C], H [auth D]	beta-D-ribopyranose C5 H10 O5 SRBFZHDQGSBBOR-TXICZTDVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.631	α = 90
b = 151.22	β = 90
c = 169.856	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-02 
Deposition Author(s): Pan, L.X., Wang, B., Yang, L.Y., Yang, D.F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31860245
National Natural Science Foundation of China (NSFC)	China	31702386

Revision History  

• Version 1.0: 2022-03-02
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description