1OB2

E. coli elongation factor EF-Tu complexed with the antibiotic kirromycin, a GTP analog, and Phe-tRNA

• PDB DOI: https://doi.org/10.2210/pdb1OB2/pdb
• NAKB: 1OB2

• Classification: HYDROLASE/NUCLEAR PROTEIN
• Organism(s): Escherichia coli BL21, Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2003-01-24 Released: 2004-05-27 
• Deposition Author(s): Kristensen, O., Nissen, P., Nyborg, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free: 
  0.265 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Kirromycin Defines a Specific Domain Arrangement of Elongation Factor EF-TU

Nielsen, R.C., Kristensen, O., Kjeldgaard, M., Thirup, S., Nissen, P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.92 kDa 
• Atom Count: 4,810 
• Modelled Residue Count: 470 
• Deposited Residue Count: 470 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ELONGATION FACTOR TU	A	393	Escherichia coli BL21	Mutation(s): 0  EC: 3.6.1.48
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12)) Explore P0CE48  Go to UniProtKB:  P0CE48

Entity ID: 2
Molecule	Chains	Length	Organism	Image
TRANSFER-RNA, PHE	B	77	Saccharomyces cerevisiae

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan:  G05551OP GlyCosmos:  G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KIR	D [auth A]	KIRROMYCIN C43 H60 N2 O12 HMSYAPGFKGSXAJ-PAHGNTJYSA-N
GNP	E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHA	B	L-PEPTIDE LINKING	C9 H11 N O		PHE

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.35 Å
• R-Value Free:  0.265 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 196.41	α = 90
b = 196.41	β = 90
c = 196.41	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
Agrovata	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-27 
Deposition Author(s): Kristensen, O., Nissen, P., Nyborg, J.

Revision History  

• Version 1.0: 2004-05-27
  Type: Initial release
  
• Version 1.1: 2012-11-14
  Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
• Version 1.2: 2015-08-19
  Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary