4I6Z | pdb_00004i6z

Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide

• PDB DOI: https://doi.org/10.2210/pdb4I6Z/pdb
• NAKB: 4I6Z

• Classification: Transcription Regulator/DNA
• Organism(s): Thermotoga maritima MSB8, synthetic construct
• 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: 3.20 Å
• R-Value Free: 
  0.268 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the transcriptional regulator TM1030 with 24bp DNA oligonucleotide

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 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 63.56 kDa 
• Atom Count: 3,606 
• Modeled Residue Count: 424 
• Deposited Residue Count: 452 
• Unique protein chains: 1
• Unique nucleic acid 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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA OLIGONUCLEOTIDE	C, D	24	synthetic construct

Small Molecules

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: 3.20 Å
• R-Value Free:  0.268 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M3VC74

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.008	α = 90
b = 45.954	β = 105.6
c = 82.51	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	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: 2015-05-20
  Changes: Derived calculations
• Version 1.2: 2015-05-27
  Changes: Source and taxonomy
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-09-20
  Changes: Data collection, Refinement description
• Version 1.6: 2023-12-06
  Changes: Data collection
• Version 1.7: 2024-11-20
  Changes: Structure summary