Download MendeleyThe 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.
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
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
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Transcription regulator RpiR family | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0H2VHQ2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | H [auth B], I [auth B] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| MXE Query on MXE | F [auth A], G [auth A] | 2-METHOXYETHANOL C3 H8 O2 XNWFRZJHXBZDAG-UHFFFAOYSA-N |  | ||
| NI Query on NI | D [auth A], K [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on 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 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 |
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 (Full details and data files)
- 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 - Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary
