4IL2 | pdb_00004il2

Crystal structure of D-mannonate dehydratase (rspA) from E. coli CFT073 (EFI TARGET EFI-501585)

• PDB DOI: https://doi.org/10.2210/pdb4IL2/pdb

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


• Deposited: 2012-12-28 Released: 2013-02-20 
• 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: 1.95 Å
• R-Value Free: 
  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

Mannonate degradation pathway in E. coli CFT073

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

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D4  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content 

• Total Structure Weight: 195.78 kDa 
• Atom Count: 12,840 
• Modeled Residue Count: 1,545 
• Deposited Residue Count: 1,704 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Starvation sensing protein rspA	A, B, C, D	426	Escherichia coli CFT073	Mutation(s): 0  Gene Names: c1971, rspA EC: 4.2.1 (UniProt), 4.2.1.8 (UniProt)
UniProt
Find proteins for Q8FHC7 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore Q8FHC7  Go to UniProtKB:  Q8FHC7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.209 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.78	α = 90
b = 123.78	β = 90
c = 112.21	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-20 
Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

Revision History  

• Version 1.0: 2013-02-20
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations