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

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
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history.

Literature

The crystal structure of Hu protein in Staphylococcus aureus

Liu, Y.H., Li, Y., Liu, B.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99U17
Sequence Annotations Expand
Reference Sequence

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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-12-06

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.