4ILK | pdb_00004ilk

Crystal structure of short chain alcohol dehydrogenase (rspB) from E. coli CFT073 (EFI TARGET EFI-506413) complexed with cofactor NADH

• PDB DOI: https://doi.org/10.2210/pdb4ILK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli CFT073
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-31 Released: 2013-01-30 
• Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.218 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

Crystal structure of short chain alcohol dehydrogenase (rspB) from E. coli CFT073 (EFI TARGET EFI-506413) complexed with cofactor NADH

Wichelecki, S., Lukk, T., Imker, H.J., Nair, S.K., Gerlt, J.A.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 79.02 kDa 
• Atom Count: 5,579 
• Modeled Residue Count: 674 
• Deposited Residue Count: 718 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Starvation sensing protein rspB	A, B	359	Escherichia coli CFT073	Mutation(s): 0  Gene Names: c1970, rspB EC: 1.1.1
UniProt
Find proteins for A0A0H2V9Q5 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V9Q5  Go to UniProtKB:  A0A0H2V9Q5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	C [auth A], F [auth B]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
ZN	E [auth A], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	D [auth A], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.218 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.322	α = 90
b = 97.133	β = 90
c = 144.101	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-30 
Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release
  
• Version 1.1: 2014-11-12
  Changes: Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations