1ZKG | pdb_00001zkg

Crystal structure of Transcriptional regulator, TETR family (tm1030) from Thermotoga maritima at 2.30 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1ZKG/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-05-02 Released: 2005-07-26 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Literature

Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.

Premkumar, L., Rife, C.L., Sri Krishna, S., McMullan, D., Miller, M.D., Abdubek, P., Ambing, E., Astakhova, T., Axelrod, H.L., Canaves, J.M., Carlton, D., Chiu, H.J., Clayton, T., DiDonato, M., Duan, L., Elsliger, M.A., Feuerhelm, J., Floyd, R., Grzechnik, S.K., Hale, J., Hampton, E., Han, G.W., Haugen, J., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Koesema, E., Kovarik, J.S., Kreusch, A., Levin, I., McPhillips, T.M., Morse, A.T., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Quijano, K., Reyes, R., Rezezadeh, F., Rodionov, D., Schwarzenbacher, R., Spraggon, G., van den Bedem, H., White, A., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2007) Proteins 68: 418-424

• PubMed: 17444523 
• DOI: https://doi.org/10.1002/prot.21436
• Primary Citation Related Structures: 
  1ZKG

---

Organizational Affiliation: 
• Burnham Institute for Medical Research, La Jolla, California, USA.

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)

Macromolecule Content 

• Total Structure Weight: 51.29 kDa 
• Atom Count: 3,347 
• Modeled Residue Count: 399 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
transcriptional regulator, TetR family	A, B	212	Thermotoga maritima MSB8	Mutation(s): 7  Gene Names: tm1030
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNL	C [auth A], D [auth B]	Unknown ligand

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: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31ZKG

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.518	α = 90
b = 87.109	β = 110.73
c = 59.156	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Data collection, Refinement description, Structure summary