2HQV

X-ray Crystal Structure of Protein AGR_C_4470 from Agrobacterium tumefaciens. Northeast Structural Genomics Consortium Target AtR92.

• PDB DOI: https://doi.org/10.2210/pdb2HQV/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-07-19 Released: 2006-09-19 
• Deposition Author(s): Vorobiev, S.M., Neely, H., Seetharaman, J., Zhao, L., Cunningham, K., Ma, L.C., Fang, Y., Xiao, R., Acton, T., Montelione, T.G., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.269 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 

Literature

Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens.

Vorobiev, S.M., Neely, H., Seetharaman, J., Ma, L.C., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L.

(2007) Protein Sci 16: 535-538

• PubMed: 17322535 
• DOI: https://doi.org/10.1110/ps.062663307
• Primary Citation of Related Structures:  
  2HQV


• PubMed Abstract: 
  

  We report here the crystal structure at 2.0 A resolution of the AGR_C_4470p protein from the Gram-negative bacterium Agrobacterium tumefaciens. The protein is a tightly associated dimer, each subunit of which bears strong structural homology with the two domains of the heme utilization protein ChuS from Escherichia coli and HemS from Yersinia enterocolitica. Remarkably, the organization of the AGR_C_4470p dimer is the same as that of the two domains in ChuS and HemS, providing structural evidence that these two proteins evolved by gene duplication. However, the binding site for heme, while conserved in HemS and ChuS, is not conserved in AGR_C_4470p, suggesting that it probably has a different function. This is supported by the presence of two homologs of AGR_C_4470p in E. coli, in addition to the ChuS protein.

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Organizational Affiliation: 

Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 21.62 kDa 
• Atom Count: 1,333 
• Modelled Residue Count: 172 
• Deposited Residue Count: 195 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AGR_C_4470p	A	195	Agrobacterium fabrum str. C58	Mutation(s): 5  Gene Names: AGR_C_4470
UniProt
Find proteins for Q7CX01 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CX01  Go to UniProtKB:  Q7CX01

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: 2.00 Å
• R-Value Free: 0.269 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.239	α = 90
b = 72.322	β = 90
c = 104.726	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-19 
Deposition Author(s): Vorobiev, S.M., Neely, H., Seetharaman, J., Zhao, L., Cunningham, K., Ma, L.C., Fang, Y., Xiao, R., Acton, T., Montelione, T.G., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2006-09-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary