8JX6 | pdb_00008jx6

Deep-Sea Helicase 9 (DSH9)

• PDB DOI: https://doi.org/10.2210/pdb8JX6/pdb

• Classification: MOTOR PROTEIN
• Organism(s): metagenome
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-06-30 Released: 2023-07-26 
• Deposition Author(s): Wang, L., Liu, Z., Guo, F.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: in silico

Literature

Structure of Deep-Sea Helicase 9 (DSH9)

Wang, L., Liu, Z., Guo, F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 105.74 kDa 
• Atom Count: 7,922 
• Modeled Residue Count: 898 
• Deposited Residue Count: 914 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deep-Sea Helicase 9	A, B	457	metagenome	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA	C [auth A], E [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
MG (Subject of Investigation/LOI)	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.808	α = 90
b = 126.836	β = 90
c = 150.715	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-07-26 
Deposition Author(s): Wang, L., Liu, Z., Guo, F.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32100994

Revision History  

• Version 1.0: 2023-07-26
  Type: Initial release
  
• Version 1.1: 2024-05-29
  Changes: Data collection
• Version 2.0: 2025-12-24
  Type: Coordinate replacement
  Reason: Ligand identity
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Structure summary