8YUN | pdb_00008yun

The crystal structure of HNBP001-HCP

• PDB DOI: https://doi.org/10.2210/pdb8YUN/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-27 Released: 2025-07-02 
• Deposition Author(s): Chen, C.Z., Xia, Q.F.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.228 (Depositor) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Repurposing of netilmicin sulfate to kill Burkholderia pseudomallei through a novel bactericidal mechanism.

Chen, C.Z., Xia, Q.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: equilibrium centrifugation

Biological Assembly 2  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 210.78 kDa 
• Atom Count: 13,300 
• Modeled Residue Count: 1,703 
• Deposited Residue Count: 1,932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hcp1 family type VI secretion system effector	A, B, C, D, E, F [auth G], G [auth K], H, I, J [auth F], K [auth L], L [auth J]	161	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: hcp, BOC38_30770, CXQ84_21600, EGY15_30370, Y036_4896
UniProt
Find proteins for Q63NX7 (Burkholderia pseudomallei (strain K96243)) Explore Q63NX7  Go to UniProtKB:  Q63NX7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.267 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.228 (Depositor) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.077	α = 89.99
b = 82.213	β = 90.307
c = 100.116	γ = 119.728

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Chen, C.Z., Xia, Q.F.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release