1NS5

X-RAY STRUCTURE OF YBEA FROM E.COLI. NORTHEAST STRUCTURAL GENOMICS RESEARCH CONSORTIUM (NESG) TARGET ER45

• PDB DOI: https://doi.org/10.2210/pdb1NS5/pdb

• Classification: Structural Genomics, Unknown Function
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-01-27 Released: 2003-02-04 
• Deposition Author(s): Benach, J., Shen, J., Rost, B., Xiao, R., Acton, T., Montelione, G., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 
  0.213 (Depositor) 
• R-Value Work: 
  0.145 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Literature

Structure of YBEA from E. coli

BENACH, J., SHEN, J., ROST, B., XIAO, R., ACTON, T., MONTELIONE, G., HUNT, J.F.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.11 kDa 
• Atom Count: 2,832 
• Modelled Residue Count: 308 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ybeA	A, B	155	Escherichia coli	Mutation(s): 4  Gene Names: ybea EC: 2.1.1.177
UniProt
Find proteins for P0A8I8 (Escherichia coli (strain K12)) Explore P0A8I8  Go to UniProtKB:  P0A8I8

Small Molecules

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: 1.68 Å
• R-Value Free:  0.213 (Depositor) 
• R-Value Work:  0.145 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.922	α = 90
b = 58.652	β = 102.15
c = 57.415	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-02-04 
Deposition Author(s): Benach, J., Shen, J., Rost, B., Xiao, R., Acton, T., Montelione, G., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2003-02-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Structure summary