6IPX | pdb_00006ipx

Crystal structure of the apo form transcription factor

• PDB DOI: https://doi.org/10.2210/pdb6IPX/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Spbetavirus SPbeta
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-05 Released: 2019-01-23 
• Deposition Author(s): Oy, S.Y., Zhen, X., Zhou, H., Ding, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free: 
  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Starting Model: experimental

Literature

Structural basis of AimP signaling molecule recognition by AimR in Spbeta group of bacteriophages.

Zhen, X., Zhou, H., Ding, W., Zhou, B., Xu, X., Perculija, V., Chen, C.J., Chang, M.X., Choudhary, M.I., Ouyang, S.

(2019) Protein Cell 10: 131-136

• PubMed: 30421358 
• DOI: https://doi.org/10.1007/s13238-018-0588-6
• Primary Citation of Related Structures:  
  6IM4, 6IPX

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Organizational Affiliation: 
• The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China.
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201204, China.
CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China.
Institute of Biotechnology, National Cheng Kung University, Tainan, 701, China.
State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan.
The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. [e-mail].
Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China. [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. [e-mail].

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 91.7 kDa 
• Atom Count: 6,415 
• Modeled Residue Count: 778 
• Deposited Residue Count: 780 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AimR transcriptional regulator	A, B	390	Spbetavirus SPbeta	Mutation(s): 0  Gene Names: aimR, yopK
UniProt
Find proteins for O64094 (Bacillus phage SPbeta) Explore O64094  Go to UniProtKB:  O64094

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.63 Å
• R-Value Free:  0.282 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.46	α = 90
b = 214.71	β = 90
c = 33.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-01-23 
Deposition Author(s): Oy, S.Y., Zhen, X., Zhou, H., Ding, W.

Revision History  

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2019-02-06
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description