4IXA | pdb_00004ixa

Structure of DNA-binding domain of the response regulator SaeR from Staphylococcus epidermidis

• PDB DOI: https://doi.org/10.2210/pdb4IXA/pdb

• Classification: TRANSCRIPTION
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-01-24 Released: 2014-01-29 
• Deposition Author(s): Chen, Y.R., Chen, S.C., Yang, C.S., Kuan, S.M., Liu, Y.H., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.262 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Structure of DNA-binding domain of the response regulator SaeR from Staphylococcus epidermidis

Chen, Y.R., Chen, S.C., Yang, C.S., Kuan, S.M., Liu, Y.H., Chen, Y.

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 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: 26.68 kDa 
• Atom Count: 1,749 
• Modeled Residue Count: 196 
• Deposited Residue Count: 220 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator SaeR	A, B	110	Staphylococcus epidermidis ATCC 12228	Mutation(s): 1  Gene Names: saeR, SE_0479
UniProt
Find proteins for Q8CQ17 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore Q8CQ17  Go to UniProtKB:  Q8CQ17

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.262 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.201	α = 90
b = 53.784	β = 90
c = 111.658	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-29 
Deposition Author(s): Chen, Y.R., Chen, S.C., Yang, C.S., Kuan, S.M., Liu, Y.H., Chen, Y.

Revision History  

• Version 1.0: 2014-01-29
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references