6K1Y | pdb_00006k1y

Crystal structure of Rhodothermus marinus substrate-binding protein at pH 7.5

PDB DOI: https://doi.org/10.2210/pdb6K1Y/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: 1.90 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.178 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6K1Y

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

Literature

Crystal structure of Rhodothermus marinus substrate-binding protein at pH 7.5

Nam, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 20.8 kDa
Atom Count: 1,256
Modeled Residue Count: 155
Deposited Residue Count: 189
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type uncharacterized transport system periplasmic component-like protein	A	189	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D0MDR1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.178 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.544	α = 90
b = 48.601	β = 90
c = 57.821	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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

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 (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.