3IWF

The Crystal Structure of the N-terminal domain of a RpiR Transcriptional Regulator from Staphylococcus epidermidis to 1.4A

• PDB DOI: https://doi.org/10.2210/pdb3IWF/pdb

• Classification: transcription regulator
• Organism(s): Staphylococcus epidermidis ATCC 12228
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-09-02 Released: 2009-09-15 
• Deposition Author(s): Stein, A.J., Sather, A., Borovilos, M., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 

Literature

The Crystal Structure of the N-terminal domain of a RpiR Transcriptional Regulator from Staphylococcus epidermidis to 1.4A

Stein, A.J., Sather, A., Borovilos, M., Bargassa, M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.47 kDa 
• Atom Count: 1,717 
• Modelled Residue Count: 179 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription regulator RpiR family	A, B	107	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0  Gene Names: SE1891, SE_1891
UniProt
Find proteins for A0A0H2VHQ2 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore A0A0H2VHQ2  Go to UniProtKB:  A0A0H2VHQ2

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	H [auth B], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MXE	F [auth A], G [auth A]	2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N
NI	D [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	C [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.205 
• R-Value Work: 0.177 
• R-Value Observed: 0.179 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.921	α = 90
b = 54.028	β = 90
c = 173.044	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-15 
Deposition Author(s): Stein, A.J., Sather, A., Borovilos, M., Bargassa, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description