1XW8 | pdb_00001xw8

X-ray structure of putative lactam utilization protein YBGL. Northeast Structural Genomics Consortium target ET90.

• PDB DOI: https://doi.org/10.2210/pdb1XW8/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-29 Released: 2004-11-09 
• Deposition Author(s): Kuzin, A.P., Chen, Y., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

X-ray structure of putative lactam utilization protein YBGL. Northeast Structural Genomics Consortium target ET90.

Kuzin, A.P., Chen, Y., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, L.

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.

Macromolecule Content

• Total Structure Weight: 27.18 kDa 
• Atom Count: 1,758 
• Modelled Residue Count: 230 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0271 protein ybgL	A	252	Escherichia coli	Mutation(s): 6  Gene Names: ybgL EC: 3.5.2.9
UniProt
Find proteins for P75746 (Escherichia coli (strain K12)) Explore P75746  Go to UniProtKB:  P75746

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.669	α = 90
b = 37.208	β = 93.97
c = 79.801	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-09 
Deposition Author(s): Kuzin, A.P., Chen, Y., Vorobiev, S.M., Acton, T.B., Ma, L.-C., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Structure summary