9JTH | pdb_00009jth

Crystal structure of NahX from Pseudomonas sp. MC1

PDB DOI: https://doi.org/10.2210/pdb9JTH/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Pseudomonas sp. MC1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-04 Released: 2025-10-08
Deposition Author(s): Son, J., Park, A.K., Kim, H.W.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.208 (Depositor), 0.207 (DCC)
R-Value Work:
0.199 (Depositor), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of NahX from Pseudomonas sp. MC1

Son, J., Park, A.K., Kim, H.W.

To be published.

Macromolecule Content

Total Structure Weight: 58.96 kDa
Atom Count: 4,473
Modeled Residue Count: 552
Deposited Residue Count: 560
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NahX	A, B, C, D	140	Pseudomonas sp. MC1	Mutation(s): 0 Gene Names: nahX, pYIC1_54
UniProt
Find proteins for G9G7K4 (Pseudomonas sp. MC1) Explore G9G7K4 Go to UniProtKB: G9G7K4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G9G7K4
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.208 (Depositor), 0.207 (DCC)
R-Value Work: 0.199 (Depositor), 0.198 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.169	α = 90
b = 108.169	β = 90
c = 198.058	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021M1A5A1075524

Revision History (Full details and data files)

Version 1.0: 2025-10-08
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.