Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 15.33 kDa 
• Atom Count: 1234 
• Modelled Residue Count: 136 
• Deposited Residue Count: 136 
• Unique protein chains: 1

1BKB

INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM

• PDB DOI: 10.2210/pdb1BKB/pdb

• Classification: TRANSLATION
• Organism(s): Pyrobaculum aerophilum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1998-07-05 Released: 1998-11-04 
• Deposition Author(s): Peat, T.S., Newman, J., Waldo, G.S., Berendzen, J., Terwilliger, T.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.236 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution.

Peat, T.S., Newman, J., Waldo, G.S., Berendzen, J., Terwilliger, T.C.

(1998) Structure 6: 1207-1214

• PubMed: 9753699 
• DOI: 10.1016/s0969-2126(98)00120-8
• Primary Citation of Related Structures:  
  1BKB


• PubMed Abstract: 
  

Translation initiation factor 5A (IF-5A) is reported to be involved in the first step of peptide bond formation in translation, to be involved in cell-cycle regulation and to be a cofactor for the Rev and Rex transactivator proteins of human immunodeficiency virus-1 and T-cell leukemia virus I, respectively. IF-5A contains an unusual amino acid, hypusine (N-epsilon-(4-aminobutyl-2-hydroxy)lysine), that is required for its function. The first step in the post-translational modification of lysine to hypusine is catalyzed by the enzyme deoxyhypusine synthase, the structure of which has been published recently.

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Organizational Affiliation: 

Life Sciences Division Los Alamos National Laboratory Mail Stop M888, Los Alamos, New Mexico, 87545, USA [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRANSLATION INITIATION FACTOR 5A	A	136	Pyrobaculum aerophilum	Mutation(s): 0
UniProt
Find proteins for P56635 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore P56635  Go to UniProtKB:  P56635

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: 1.75 Å
• R-Value Free: 0.236 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.13	α = 90
b = 114.13	β = 90
c = 32.59	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing
DENZO	data reduction
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-05 
• Released Date: 1998-11-04 
Deposition Author(s): Peat, T.S., Newman, J., Waldo, G.S., Berendzen, J., Terwilliger, T.C.

Revision History  

• Version 1.0: 1998-11-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance