2CX0 | pdb_00002cx0

Crystal structure of a PUA domain (APE0525) from the Aeropyrum pernix K1 (sulfate complex)

• PDB DOI: https://doi.org/10.2210/pdb2CX0/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Aeropyrum pernix K1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-27 Released: 2005-12-27 
• Deposition Author(s): Mizohata, E., Morita, S., Nagano, K., Uda, H., 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: 
  0.199 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Literature

Crystal structure of a PUA domain (APE0525) from the Aeropyrum pernix K1 (sulfate complex)

Mizohata, E., Morita, S., Nagano, K., Uda, H., 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: 21.14 kDa 
• Atom Count: 1,608 
• Modeled Residue Count: 184 
• Deposited Residue Count: 187 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein APE0525	A	187	Aeropyrum pernix K1	Mutation(s): 3  Gene Names: APE0525
UniProt
Find proteins for Q9YEQ6 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YEQ6  Go to UniProtKB:  Q9YEQ6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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:  0.199 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.331	α = 90
b = 48.135	β = 102.5
c = 53.847	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-27 
Deposition Author(s): Mizohata, E., Morita, S., Nagano, K., Uda, H., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2005-12-27
  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: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary