3L6I | pdb_00003l6i

Crystal structure of the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542

• PDB DOI: https://doi.org/10.2210/pdb3L6I/pdb
• Entry: 3L6I supersedes: 3EYR

• Classification: structure genomics, unknown function
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-23 Released: 2010-01-26 
• Deposition Author(s): Kuzin, A.P., Neely, H., Seetharaman, J., Chen, C.X., Janjua, H., Cunningham, K., 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: 2.01 Å
• R-Value Free: 
  0.247 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Literature

Crystal structure of the uncharacterized lipoprotein yceb from e. coli at the resolution 2.0a. northeast structural genomics consortium target er542

Kuzin, A.P., Neely, H., Seetharaman, J., Chen, C.X., Janjua, H., Cunningham, K., 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: 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.53 kDa 
• Atom Count: 2,837 
• Modelled Residue Count: 343 
• Deposited Residue Count: 362 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized lipoprotein yceB	A, B	181	Escherichia coli K-12	Mutation(s): 0  Gene Names: yceB, b1063, JW1050
UniProt
Find proteins for P0AB26 (Escherichia coli (strain K12)) Explore P0AB26  Go to UniProtKB:  P0AB26

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [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: 2.01 Å
• R-Value Free:  0.247 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.05	α = 90
b = 174.55	β = 90
c = 43.8	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SnB	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-26 
Deposition Author(s): Kuzin, A.P., Neely, H., Seetharaman, J., Chen, C.X., Janjua, H., Cunningham, K., 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)
• This entry supersedes: 3EYR

Revision History  

• Version 1.0: 2010-01-26
  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: 2017-11-01
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary