3R79 | pdb_00003r79

Crystal structure of an uncharactertized protein from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3R79/pdb

• Classification: Structure Genomics, unknown function
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-22 Released: 2011-04-06 
• Deposition Author(s): Eswaramoorthy, S., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.212 (DCC) 

Literature

Crystal structure of an uncharactertized protein from Agrobacterium tumefaciens

Eswaramoorthy, S., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.84 kDa 
• Atom Count: 3,606 
• Modeled Residue Count: 449 
• Deposited Residue Count: 488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
uncharacterized protein	A, B	244	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_4983, Atu2747, PLPDE_III_YBL036c_like
UniProt
Find proteins for A9CHE9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHE9  Go to UniProtKB:  A9CHE9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PR	C [auth A], D [auth B]	PRASEODYMIUM ION Pr WCWKKSOQLQEJTE-UHFFFAOYSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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: 1.90 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.212 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.687	α = 90
b = 89.128	β = 90
c = 109.731	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
SHARP	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Eswaramoorthy, S., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-22
  Changes: Structure summary
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary