2GP4

Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis

• PDB DOI: https://doi.org/10.2210/pdb2GP4/pdb

• Classification: LYASE
• Organism(s): Shewanella oneidensis MR-1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-04-16 Released: 2006-05-09 
• Deposition Author(s): Schormann, N., Symersky, J., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.291 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 

Literature

Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis

Schormann, N., Symersky, J., Karpova, E., Zhang, Y., Lu, S., Qiu, S., Bunzel, R., Luan, C.-H., Huang, W., Luo, M., Tsao, J., Johnson, D., Carson, M., Zhou, Q., Luo, D., Gray, R., Cao, Z., An, J., Arabshahi, A., Li, S., Stinnett, M., McKinstry, A., Lin, G., Shang, Q., Chen, Y., DeLucas, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135.39 kDa 
• Atom Count: 8,116 
• Modelled Residue Count: 1,018 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphogluconate dehydratase	A, B	628	Shewanella oneidensis MR-1	Mutation(s): 17  Gene Names: edd EC: 4.2.1.12
UniProt
Find proteins for Q8EEA0 (Shewanella oneidensis (strain MR-1)) Explore Q8EEA0  Go to UniProtKB:  Q8EEA0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.291 
• R-Value Work: 0.230 
• R-Value Observed: 0.233 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.364	α = 90
b = 118.649	β = 90
c = 160.017	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-09 
Deposition Author(s): Schormann, N., Symersky, J., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2006-05-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance