4I76 | pdb_00004i76

Crystal structure of transcriptional regulator TM1030 with octanol

• PDB DOI: https://doi.org/10.2210/pdb4I76/pdb

• Classification: Transcription Regulator
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-30 Released: 2013-01-02 
• Deposition Author(s): Koclega, K.D., Chruszcz, M., Cooper, D.R., Petkowski, J.J., Tkaczuk, K.L., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of transcriptional regulator TM1030 with octanol

Koclega, K.D., Chruszcz, M., Cooper, D.R., Petkowski, J.J., Tkaczuk, K.L., Joachimiak, A., Minor, W.

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 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.26 kDa 
• Atom Count: 3,593 
• Modeled Residue Count: 398 
• Deposited Residue Count: 404 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B	202	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM1030, TM_1030
UniProt
Find proteins for Q9X0C0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X0C0  Go to UniProtKB:  Q9X0C0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OC9	C [auth A], D [auth A]	OCTAN-1-OL C8 H18 O KBPLFHHGFOOTCA-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], 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: 2.10 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3PP4J

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.911	α = 90
b = 50.429	β = 129.15
c = 88.098	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-02 
Deposition Author(s): Koclega, K.D., Chruszcz, M., Cooper, D.R., Petkowski, J.J., Tkaczuk, K.L., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2013-01-02
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection
• Version 1.5: 2024-11-27
  Changes: Structure summary