2CXH

Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1

• PDB DOI: https://doi.org/10.2210/pdb2CXH/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-29 Released: 2005-12-29 
• Deposition Author(s): Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 

Literature

Crystal structure of probable ribosomal biogenesis protein from Aeropyrum pernix K1

Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.77 kDa 
• Atom Count: 1,540 
• Modelled Residue Count: 180 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable brix-domain ribosomal biogenesis protein	A	217	Aeropyrum pernix K1	Mutation(s): 4  Gene Names: APE1443
UniProt
Find proteins for Q9YC08 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YC08  Go to UniProtKB:  Q9YC08

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.209 
• R-Value Work: 0.184 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.171	α = 90
b = 47.364	β = 90
c = 124.675	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-29 
Deposition Author(s): Kawazoe, M., Takemoto, C., Hanawa-Suetsugu, K., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-29
  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: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary