5VM2 | pdb_00005vm2

Crystal structure of ECK1772, an oxidoreductase/dehydrogenase of unknown specificity involved in membrane biogenesis from Escherichia coli

• PDB DOI: https://doi.org/10.2210/pdb5VM2/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-26 Released: 2017-06-07 
• Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Di Leo, R., Savchenko, A., Anderson, W.F., 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: 1.98 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of ECK1772, an oxidoreductase/dehydrogenase of unknown specificity involved in membrane biogenesis from Escherichia coli

Stogios, P.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 75.71 kDa 
• Atom Count: 5,986 
• Modeled Residue Count: 694 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alcohol dehydrogenase	A, B	347	Escherichia coli	Mutation(s): 0  Gene Names: ARC77_00615, AU473_19815, BFL24_13020, ECs2483 EC: 1
UniProt
Find proteins for P77280 (Escherichia coli (strain K12)) Explore P77280  Go to UniProtKB:  P77280

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35vm2

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.994	α = 90
b = 70.888	β = 90
c = 149.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Stogios, P.J., Skarina, T., McChesney, C., Di Leo, R., Savchenko, A., Anderson, W.F., 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	HHSCN27220120026C

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-11-15
  Changes: Data collection
• Version 1.5: 2024-10-23
  Changes: Structure summary