6K1W | pdb_00006k1w

Crystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5

• PDB DOI: https://doi.org/10.2210/pdb6K1W/pdb

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


• Deposited: 2019-05-13 Released: 2019-08-21 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Rhodothermus marinus substrate-binding protein at pH 5.5

Nam, K.H.

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

Macromolecule Content 

• Total Structure Weight: 18.39 kDa 
• Atom Count: 1,291 
• Modeled Residue Count: 149 
• Deposited Residue Count: 168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type uncharacterized transport system periplasmic component-like protein	A	168	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.421	α = 90
b = 48.613	β = 90
c = 58.111	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-21 
Deposition Author(s): Nam, K.H.

---

Funding Organization	Location	Grant Number
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087
National Research Foundation (Korea)	Korea, Republic Of	NRF-2017M3A9F6029736

Revision History  

• Version 1.0: 2019-08-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description