5TJJ | pdb_00005tjj

Crystal structure of IcIR transcriptional regulator from Alicyclobacillus acidocaldarius

• PDB DOI: https://doi.org/10.2210/pdb5TJJ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-04 Released: 2016-10-26 
• Deposition Author(s): Michalska, K., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.234 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Literature

Crystal structure of IcIR transcriptional regulator from Alicyclobacillus acidocaldarius

Michalska, K., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 58.14 kDa 
• Atom Count: 3,999 
• Modeled Residue Count: 504 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, IclR family	A, B	260	Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446	Mutation(s): 0  Gene Names: Aaci_0162
UniProt
Find proteins for C8WQP8 (Alicyclobacillus acidocaldarius subsp. acidocaldarius (strain ATCC 27009 / DSM 446 / BCRC 14685 / JCM 5260 / KCTC 1825 / NBRC 15652 / NCIMB 11725 / NRRL B-14509 / 104-IA)) Explore C8WQP8  Go to UniProtKB:  C8WQP8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.50 Å
• R-Value Free:  0.234 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35tjj

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.38	α = 90
b = 98.38	β = 90
c = 119.485	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
BUCCANEER	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Michalska, K., Mack, J.C., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM094585

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Structure summary