3D3O | pdb_00003d3o

Crystal structure of the effector domain of the putative transcriptional regulator IclR from Acinetobacter sp. ADP1

• PDB DOI: https://doi.org/10.2210/pdb3D3O/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Acinetobacter baylyi ADP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-12 Released: 2008-07-08 
• Deposition Author(s): Kim, Y., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal Structure of the Effector Domain of the Putative Transcriptional Regulator IclR from Acinetobacter sp. ADP1.

Kim, Y., Shackelford, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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)

Macromolecule Content 

• Total Structure Weight: 41.55 kDa 
• Atom Count: 2,986 
• Modeled Residue Count: 348 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative transcriptional regulator, IcIR family	A, B	178	Acinetobacter baylyi ADP1	Mutation(s): 0  Gene Names: ACIAD1822
UniProt
Find proteins for Q6FBA6 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore Q6FBA6  Go to UniProtKB:  Q6FBA6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NH4	H [auth B]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

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: 2.46 Å
• R-Value Free:  0.269 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.382	α = 90
b = 71.681	β = 90
c = 96.222	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Kim, Y., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary