6OZ7 | pdb_00006oz7

Putative oxidoreductase from Escherichia coli str. K-12

• PDB DOI: https://doi.org/10.2210/pdb6OZ7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2019-05-15 Released: 2019-05-29 
• Deposition Author(s): Osipiuk, J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 
  0.126 (Depositor) 

Starting Model: experimental

Literature

Putative oxidoreductase from Escherichia coli str. K-12

Osipiuk, J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 217.19 kDa 
• Atom Count: 16,852 
• Modeled Residue Count: 1,912 
• Deposited Residue Count: 2,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized oxidoreductase YohF	A, B, C, D, E, F, G, H	254	Escherichia coli K-12	Mutation(s): 0  Gene Names: yohF, yohE, b2137, JW2125 EC: 1
UniProt
Find proteins for P33368 (Escherichia coli (strain K12)) Explore P33368  Go to UniProtKB:  P33368

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	L [auth C], N [auth D]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
EDO	P [auth E], Q [auth E], T [auth H]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	I [auth A], J [auth B], K [auth C], M [auth D], O [auth E], R [auth F], S [auth G], U [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.123 (DCC) 
• R-Value Observed: 0.126 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36oz7

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.819	α = 82.59
b = 72.21	β = 87.03
c = 119.945	γ = 67.82

Software Package:

Software Name	Purpose
HKL-3000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-05-29 
Deposition Author(s): Osipiuk, J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201200026C
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2019-05-29
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description