2CY1 | pdb_00002cy1

Crystal structure of APE1850

• PDB DOI: https://doi.org/10.2210/pdb2CY1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-04 Released: 2006-01-04 
• Deposition Author(s): Shibata, R., Bessho, Y., Umehara, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystallization of the archaeal transcription termination factor NusA: a significant decrease in twinning under microgravity conditions

Tanaka, H., Umehara, T., Inaka, K., Takahashi, S., Shibata, R., Bessho, Y., Sato, M., Sugiyama, S., Fusatomi, E., Terada, T., Shirouzu, M., Sano, S., Motohara, M., Kobayashi, T., Tanaka, T., Tanaka, A., Yokoyama, S.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 69-73

• PubMed: 17277442 
• DOI: https://doi.org/10.1107/S1744309106054625
• Primary Citation Related Structures: 
  2CY1


• PubMed Abstract: 
  

  The transcription termination factor NusA from Aeropyrum pernix was crystallized using a counter-diffusion technique in both terrestrial and microgravity environments. Crystallization under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 A, with similar unit-cell parameters. Based on a comparison of the crystal parameters, the effect of microgravity on protein crystallization is discussed.

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Organizational Affiliation: 
• Confocal Science Inc., Wakamatsu Building 7F, 3-3-6 Nihonbashi Hon-cho, Chuo-ku, Tokyo 103-0023, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 16.07 kDa 
• Atom Count: 1,105 
• Modeled Residue Count: 138 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NusA protein homolog	A	144	Aeropyrum pernix K1	Mutation(s): 0
UniProt
Find proteins for Q9YAU4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YAU4  Go to UniProtKB:  Q9YAU4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.264 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.77	α = 90
b = 99.77	β = 90
c = 45.812	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-04 
Deposition Author(s): Shibata, R., Bessho, Y., Umehara, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2006-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description