3S5R | pdb_00003s5r

Crystal structure of a putative transcriptional regulator of the TETR family (SYN_02108) from Syntrophus aciditrophicus at 2.60 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3S5R/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Syntrophus aciditrophicus SB
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-23 Released: 2011-06-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.255 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Literature

Crystal structure of a Putative transcriptional regulator of the TetR family (SYN_02108) from Syntrophus aciditrophicus SB at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.3 kDa 
• Atom Count: 2,977 
• Modeled Residue Count: 393 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator TetR family	A, B	216	Syntrophus aciditrophicus SB	Mutation(s): 0  Gene Names: SYNAS_10510, SYN_02108
UniProt
Find proteins for Q2LS68 (Syntrophus aciditrophicus (strain SB)) Explore Q2LS68  Go to UniProtKB:  Q2LS68

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A], G [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-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: 2.60 Å
• R-Value Free:  0.255 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33S5R

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.433	α = 90
b = 110.721	β = 90
c = 126.03	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2011-06-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Structure summary