1Z0T | pdb_00001z0t

Crystal Structure of A. fulgidus Lon proteolytic domain

• PDB DOI: https://doi.org/10.2210/pdb1Z0T/pdb

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


• Deposited: 2005-03-02 Released: 2005-08-02 
• Deposition Author(s): Dauter, Z., Botos, I., LaRonde-LeBlanc, N., Wlodawer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.330 (Depositor), 0.343 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Pathological crystallography: case studies of several unusual macromolecular crystals.

Dauter, Z., Botos, I., LaRonde-LeBlanc, N., Wlodawer, A.

(2005) Acta Crystallogr D Biol Crystallogr 61: 967-975

• PubMed: 15983420 
• DOI: https://doi.org/10.1107/S0907444905011285
• Primary Citation Related Structures: 
  1Z0T, 1Z0V


• PubMed Abstract: 
  

  Although macromolecular crystallography is rapidly becoming largely routine owing to advances in methods of data collection, structure solution and refinement, difficult cases are still common. To remind structural biologists about the kinds of crystallographic difficulties that might be encountered, case studies of several successfully completed structure determinations that utilized less than perfect crystals are discussed here. The structure of the proteolytic domain of Archaeoglobus fulgidus Lon was solved with crystals that contained superimposed orthorhombic and monoclinic lattices, a case not previously described for proteins. Another hexagonal crystal form of this protein exhibited an unusually high degree of non-isomorphism. Crystals of A. fulgidus Rio1 kinase exhibited both pseudosymmetry and twinning. Ways of identifying the observed phenomena and approaches to solving and refining macromolecular structures when only less than perfect crystals are available are discussed here.

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Organizational Affiliation: 
• Synchrotron Radiation Research Section, Macromolecular Crystallography Laboratory, National Cancer Institute and Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 131.04 kDa 
• Atom Count: 9,870 
• Modeled Residue Count: 1,174 
• Deposited Residue Count: 1,230 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative protease La homolog type	A, B, C, D, E, F	205	Archaeoglobus fulgidus	Mutation(s): 0  EC: 3.4.21.53 (PDB Primary Data), 3.4.21 (UniProt)
UniProt
Find proteins for O29883 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29883  Go to UniProtKB:  O29883

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.330 (Depositor), 0.343 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.252	α = 90
b = 90.554	β = 90
c = 147.951	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-02 
Deposition Author(s): Dauter, Z., Botos, I., LaRonde-LeBlanc, N., Wlodawer, A.

Revision History  

• Version 1.0: 2005-08-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references