3LUR | pdb_00003lur

Crystal structure of Putative bacterial transcription regulation protein (NP_372959.1) from Staphylococcus aureus MU50 at 1.81 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3LUR/pdb

• Classification: Transcription activator
• Organism(s): Staphylococcus aureus subsp. aureus Mu50
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-18 Released: 2010-03-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of Putative bacterial transcription regulation protein (NP_372959.1) from Staphylococcus aureus MU50 at 1.81 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.03 kDa 
• Atom Count: 4,260 
• Modeled Residue Count: 469 
• Deposited Residue Count: 474 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative bacterial transcription regulation protein	A, B, C	158	Staphylococcus aureus subsp. aureus Mu50	Mutation(s): 0  Gene Names: SAV2435
UniProt
Find proteins for A0A0H3K0Y5 (Staphylococcus aureus (strain Mu50 / ATCC 700699)) Explore A0A0H3K0Y5  Go to UniProtKB:  A0A0H3K0Y5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	D [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG	J [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], N [auth C], O [auth C], P [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.218 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LUR

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.179	α = 90
b = 62.482	β = 93.33
c = 105.075	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-03-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary