8WXN

Crystal structure of substrate-binding protein from Rhodothermus marinus (Dose II)

PDB DOI: https://doi.org/10.2210/pdb8WXN/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Rhodothermus marinus DSM 4252
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-10-30 Released: 2023-11-22
Deposition Author(s): Nam, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.259
R-Value Work: 0.222
R-Value Observed: 0.224

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Radiation Damage on Selenomethionine-Substituted Single-Domain Substrate-Binding Protein.

(2023) Crystals (Basel) 13: 1620-1620

DOI: https://doi.org/10.3390/cryst13121620

Macromolecule Content

Total Structure Weight: 36.24 kDa
Atom Count: 2,541
Modelled Residue Count: 312
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type uncharacterized transport system periplasmic component-like protein	A, B	164	Rhodothermus marinus DSM 4252	Mutation(s): 0 Gene Names: Rmar_2176
UniProt
Find proteins for D0MDR1 (Rhodothermus marinus (strain ATCC 43812 / DSM 4252 / R-10)) Explore D0MDR1 Go to UniProtKB: D0MDR1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D0MDR1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.259
R-Value Work: 0.222
R-Value Observed: 0.224
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.552	α = 90
b = 64.164	β = 96.07
c = 69.863	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-11-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1I1A1A01050838
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2020M3H1A1075314

Revision History (Full details and data files)

Version 1.0: 2023-11-22
Type: Initial release
Version 1.1: 2024-04-17
Changes: Database references

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 R01GM133198.