8HD5 | pdb_00008hd5

The crystal structure of Hu protein in Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb8HD5/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1
• Mutation(s): No 


• Deposited: 2022-11-03 Released: 2023-12-06 
• Deposition Author(s): Liu, Y.H., Chen, H., Li, Y., Liu, B.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

The crystal structure of Hu protein in Staphylococcus aureus

Liu, Y.H., Li, Y., Liu, B.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 38.57 kDa 
• Atom Count: 2,789 
• Modeled Residue Count: 360 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein HU	A, B [auth C], C [auth B], D	90	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: hup, SAV1473
UniProt
Find proteins for Q99U17 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore Q99U17  Go to UniProtKB:  Q99U17

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.427	α = 90
b = 82.369	β = 93.157
c = 61.633	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-06 
Deposition Author(s): Liu, Y.H., Chen, H., Li, Y., Liu, B.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	2020M682420

Revision History  

• Version 1.0: 2023-12-06
  Type: Initial release
  
• Version 2.0: 2025-08-20
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary