1YNB

crystal structure of genomics APC5600

• PDB DOI: https://doi.org/10.2210/pdb1YNB/pdb

• Classification: HYDROLASE
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-24 Released: 2005-03-08 
• Deposition Author(s): Dong, A., Skarina, T., Savchenko, A., Pai, E.F., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.243 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Crystal structure of genomics AF1432 by Sulfur SAD methods

Dong, A., Skarina, T., Savchenko, A., Pai, E.F., Edwards, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 59.54 kDa 
• Atom Count: 4,303 
• Modelled Residue Count: 501 
• Deposited Residue Count: 519 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein AF1432	A, B, C	173	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: AF1432 EC: 3.1.3.89
UniProt
Find proteins for O28840 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28840  Go to UniProtKB:  O28840

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.243 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.32	α = 90
b = 131.41	β = 117.2
c = 58.56	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-08 
Deposition Author(s): Dong, A., Skarina, T., Savchenko, A., Pai, E.F., Joachimiak, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2011-10-05
  Changes: Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references