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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.236 (Depositor), 0.235 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A4XMB7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BR Query on BR Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
URE (Subject of Investigation/LOI) Query on URE Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.236 (Depositor), 0.235 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.