3IGR | pdb_00003igr

The Crystal Structure of Ribosomal-protein-S5-alanine Acetyltransferase from Vibrio fischeri to 2.0A

• PDB DOI: https://doi.org/10.2210/pdb3IGR/pdb

• Classification: TRANSFERASE
• Organism(s): Aliivibrio fischeri ES114
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-07-28 Released: 2009-09-01 
• Deposition Author(s): Stein, A.J., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

The Crystal Structure of Ribosomal-protein-S5-alanine Acetyltransferase from Vibrio fischeri to 2.0A

Stein, A.J., Sather, A., Shackelford, G., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.83 kDa 
• Atom Count: 3,182 
• Modeled Residue Count: 366 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal-protein-S5-alanine N-acetyltransferase	A, B	184	Aliivibrio fischeri ES114	Mutation(s): 0  Gene Names: rimJ, VFA0750, VF_A0750 EC: 2.3.1.128 (PDB Primary Data), 2.3.1.267 (UniProt)
UniProt
Find proteins for Q5DZH6 (Aliivibrio fischeri (strain ATCC 700601 / ES114)) Explore Q5DZH6  Go to UniProtKB:  Q5DZH6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A], D [auth A], E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.504	α = 90
b = 107.173	β = 90
c = 145.719	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Stein, A.J., Sather, A., Shackelford, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary