3CWR | pdb_00003cwr

Crystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3CWR/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Rhodospirillum rubrum ATCC 11170
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-22 Released: 2008-05-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Literature

Crystal structure of transcriptional regulator of TetR family (YP_425770.1) from Rhodospirillum rubrum ATCC 11170 at 1.50 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 generated by PISA (software)

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: 45.81 kDa 
• Atom Count: 3,277 
• Modeled Residue Count: 383 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B	208	Rhodospirillum rubrum ATCC 11170	Mutation(s): 0  Gene Names: YP_425770.1, Rru_A0679
UniProt
Find proteins for Q2RWL2 (Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1)) Explore Q2RWL2  Go to UniProtKB:  Q2RWL2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth B]	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: 1.50 Å
• R-Value Free:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.149 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33CWR

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.34	α = 90
b = 53.34	β = 90
c = 234.24	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
ADSC	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary