3SY1 | pdb_00003sy1

Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR70

• PDB DOI: https://doi.org/10.2210/pdb3SY1/pdb

• Classification: pyridoxal phosphate binding
• Organism(s): Escherichia coli K-12
• Mutation(s): Yes 


• Deposited: 2011-07-15 Released: 2011-08-03 
• Deposition Author(s): Vorobiev, S., Su, M., Nivon, L., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Baker, D., Everett, J.K., Nair, R., Acton, T.B., Rost, 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: 1.47 Å
• R-Value Free: 
  0.191 (Depositor), 0.183 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR70

Vorobiev, S., Su, M., Nivon, L., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Baker, D., Everett, J.K., Nair, R., Acton, T.B., Rost, 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: 27.34 kDa 
• Atom Count: 2,171 
• Modeled Residue Count: 229 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0001 protein yggS	A	245	Escherichia coli K-12	Mutation(s): 10  Gene Names: yggS, b2951, JW2918
UniProt
Find proteins for P67080 (Escherichia coli (strain K12)) Explore P67080  Go to UniProtKB:  P67080

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	B [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ACY	C [auth A], D [auth A], E [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.191 (Depositor), 0.183 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.715	α = 90
b = 61.695	β = 90
c = 83.234	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-03 
Deposition Author(s): Vorobiev, S., Su, M., Nivon, L., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Baker, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2011-08-03
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description