4LT9 | pdb_00004lt9

Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR404

• PDB DOI: https://doi.org/10.2210/pdb4LT9/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-23 Released: 2013-08-14 
• Deposition Author(s): Vorobiev, S., Su, M., Bjelic, S., Kipnis, Y., Wang, L., Sahdev, S., Xiao, R., Kogan, S., Maglaqui, M., Baker, D., Everett, J.K., Acton, T.B., 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: 2.15 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Engineered Protein OR404.

Vorobiev, S., Su, M., Bjelic, S., Kipnis, Y., Wang, L., Sahdev, S., Xiao, R., Kogan, S., Maglaqui, M., Baker, D., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.08 kDa 
• Atom Count: 2,056 
• Modeled Residue Count: 250 
• Deposited Residue Count: 269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Protein OR404	A	269	synthetic construct	Mutation(s): 0

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: 2.15 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.287	α = 90
b = 73.333	β = 90
c = 80.738	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
RAPD	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Vorobiev, S., Su, M., Bjelic, S., Kipnis, Y., Wang, L., Sahdev, S., Xiao, R., Kogan, S., Maglaqui, M., Baker, D., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Structure summary