3D01 | pdb_00003d01

Crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3D01/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-04-30 Released: 2008-07-01 
• Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

The crystal structure of the protein Atu1372 with unknown function from Agrobacterium tumefaciens.

Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 210.91 kDa 
• Atom Count: 15,234 
• Modeled Residue Count: 1,888 
• Deposited Residue Count: 1,980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H, I, J, K, L	165	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: GI:17935272, AGR_C_2535, Atu1372
UniProt
Find proteins for A9CJ63 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CJ63  Go to UniProtKB:  A9CJ63

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	M [auth A], N [auth B], O [auth C], P [auth E], Q [auth F], R [auth G], S [auth H], T [auth I], U [auth J], V [auth J], W [auth K], X [auth L]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.623	α = 68.2
b = 93.6	β = 67.87
c = 93.628	γ = 68.14

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-01 
Deposition Author(s): Zhang, R., Xu, X., Gu, J., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2008-07-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary