3BB6

Crystal structure of the P64488 protein from E.coli (strain K12). Northeast Structural Genomics Consortium target ER596

• PDB DOI: https://doi.org/10.2210/pdb3BB6/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-09 Released: 2007-11-20 
• Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Janjua, H., Owens, L., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

X-Ray structure of the P64488 from E.coli (strain K12).

Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Janjua, H., Owens, L., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

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: 59.81 kDa 
• Atom Count: 3,716 
• Modelled Residue Count: 436 
• Deposited Residue Count: 508 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein yeaR	A, B, C, D	127	Escherichia coli K-12	Mutation(s): 0  Gene Names: yeaR, b1797, JW1786
UniProt
Find proteins for P64488 (Escherichia coli (strain K12)) Explore P64488  Go to UniProtKB:  P64488

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth B], G [auth C], H [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.943	α = 90
b = 82.472	β = 90
c = 109.924	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SnB	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Kuzin, A.P., Su, M., Seetharaman, J., Wang, D., Janjua, H., Owens, L., Ma, L.-C., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary