8TG1 | pdb_00008tg1

Caldicellulosiruptor saccharolyticus periplasmic urea-binding protein

• PDB DOI: https://doi.org/10.2210/pdb8TG1/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Caldicellulosiruptor saccharolyticus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-12 Released: 2024-06-19 
• Deposition Author(s): Allert, M.J., Kumar, S., Wang, Y., Beese, L.S., Hellinga, H.W.
• Funding Organization(s): Becton-Dickinson and Company

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure-based functional analysis reveals multiple roles and widespread use of urea-binding proteins in nitrogen metabolism

Allert, M.J., Kumar, S., Wang, Y., Beese, L.S., Hellinga, H.W.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 87.68 kDa 
• Atom Count: 6,860 
• Modeled Residue Count: 743 
• Deposited Residue Count: 786 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Extracellular ligand-binding receptor	A, B	393	Caldicellulosiruptor saccharolyticus	Mutation(s): 0  Gene Names: Csac_2475
UniProt
Find proteins for A4XMB7 (Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)) Explore A4XMB7  Go to UniProtKB:  A4XMB7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
URE (Subject of Investigation/LOI)	C [auth A], E [auth B]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.235	α = 90
b = 91.67	β = 90
c = 96.546	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-19 
Deposition Author(s): Allert, M.J., Kumar, S., Wang, Y., Beese, L.S., Hellinga, H.W.

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Funding Organization	Location	Grant Number
Becton-Dickinson and Company	United States	--

Revision History  

• Version 1.0: 2024-06-19
  Type: Initial release