1R4V | pdb_00001r4v

1.9A crystal structure of protein AQ328 from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb1R4V/pdb

• Classification: Structural genomics, unknown function
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2003-10-08 Released: 2004-03-30 
• Deposition Author(s): Qiu, Y., Tereshko, V., Kim, Y., Zhang, R., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Literature

The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.

Qiu, Y., Tereshko, V., Kim, Y., Zhang, R., Collart, F., Yousef, M., Kossiakoff, A., Joachimiak, A.

(2006) Proteins 62: 8-16

• PubMed: 16287087 
• DOI: https://doi.org/10.1002/prot.20590
• Primary Citation Related Structures: 
  1R4V


• PubMed Abstract: 
  

  The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB code 1F1E) with z-score 8.1 and RMSD 3.6 A over 124 residues. A sedimentation equilibrium experiment indicates that Aq_328 is a monomer in solution, with an average sedimentation coefficient of 2.4 and an apparent molecular weight of about 20 kDa. The overall architecture of Aq_328 consists of two noncanonical histone domains in tandem repeat within a single chain, and is similar to eukaryotic heterodimer (H2A/H2B and H3/H4) and an archaeal histone heterodimer (HMfA/HMfB). The sequence comparisons between the two histone domains of Aq_328 and six eukaryotic/archaeal histones demonstrate that most of the conserved residues that underlie the Aq_328 architecture are used to build and stabilize the two cross-shaped antiparallel histone domains. The high percentage of salt bridges in the structure could be a factor in the protein's thermostability. The structural similarities to other histone-like proteins, molecular properties, and potential function of Aq_328 are discussed in this paper.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.48 kDa 
• Atom Count: 1,458 
• Modeled Residue Count: 151 
• Deposited Residue Count: 171 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein AQ_328	A	171	Aquifex aeolicus VF5	Mutation(s): 7  Gene Names: AQ_328
UniProt
Find proteins for O66665 (Aquifex aeolicus (strain VF5)) Explore O66665  Go to UniProtKB:  O66665

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAC	D [auth A]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
ZN	B [auth A], C [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.213 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.036	α = 90
b = 56.036	β = 90
c = 244.768	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Qiu, Y., Tereshko, V., Kim, Y., Zhang, R., Collart, F., Joachimiak, A., Kossiakoff, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary