3IWF | pdb_00003iwf

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 (Depositor), 0.202 (DCC)
R-Value Work:
0.177 (Depositor), 0.173 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2VHQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	H [auth B], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain H [auth B] Focus chain I [auth B]
MXE Query on MXE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-METHOXYETHANOL C₃ H₈ O₂ XNWFRZJHXBZDAG-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain K [auth B]	D [auth A], K [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain K [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain J [auth B]	C [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain J [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A]

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 (Depositor), 0.202 (DCC)
R-Value Work: 0.177 (Depositor), 0.173 (DCC)
R-Value Observed: 0.179 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2009-09-15

Deposition Author(s):

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