3MOG | pdb_00003mog

Crystal structure of 3-hydroxybutyryl-CoA dehydrogenase from Escherichia coli K12 substr. MG1655

• PDB DOI: https://doi.org/10.2210/pdb3MOG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2010-04-22 Released: 2010-06-23 
• Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.266 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Crystal Structure of 3-Hydroxybutyryl-Coa Dehydrogenase from Escherichia Coli K12

Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 158.56 kDa 
• Atom Count: 11,211 
• Modeled Residue Count: 1,412 
• Deposited Residue Count: 1,449 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable 3-hydroxybutyryl-CoA dehydrogenase	A, B, C	483	Escherichia coli K-12	Mutation(s): 0  Gene Names: paaH, ydbU, b1395, JW1390 EC: 1.1.1.157 (PDB Primary Data), 1.1.1 (UniProt)
UniProt
Find proteins for P76083 (Escherichia coli (strain K12)) Explore P76083  Go to UniProtKB:  P76083

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth B], H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A], E [auth B], G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.266 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.302	α = 90
b = 145.753	β = 90
c = 148.783	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-23 
Deposition Author(s): Patskovsky, Y., Ramagopal, U., Toro, R., Gilmore, M., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references