3C2B | pdb_00003c2b

Crystal structure of TetR transcriptional regulator from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3C2B/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-01-24 Released: 2008-02-05 
• Deposition Author(s): Osipiuk, J., Skarina, T., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

X-ray crystal structure of TetR transcriptional regulator from Agrobacterium tumefaciens.

Osipiuk, J., Skarina, T., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 48.71 kDa 
• Atom Count: 3,192 
• Modeled Residue Count: 394 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, TetR family	A, B	221	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: Atu2020, AGR_C_3662
UniProt
Find proteins for A9CID8 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CID8  Go to UniProtKB:  A9CID8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-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:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.134	α = 90
b = 72.791	β = 90
c = 127.198	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
CNS	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-05 
Deposition Author(s): Osipiuk, J., Skarina, T., Zheng, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-02-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary