5DZS

1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.

• PDB DOI: https://doi.org/10.2210/pdb5DZS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-26 Released: 2015-10-07 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Starting Model: experimental

Literature

1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.

Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 62.48 kDa 
• Atom Count: 5,100 
• Modelled Residue Count: 533 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Shikimate dehydrogenase (NADP(+))	A, B	276	Clostridioides difficile 630	Mutation(s): 0  Gene Names: aroE1, CD630_18370 EC: 1.1.1.25
UniProt
Find proteins for Q187E7 (Clostridioides difficile (strain 630)) Explore Q187E7  Go to UniProtKB:  Q187E7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m35dzs

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.221	α = 77.98
b = 47.053	β = 76.44
c = 74.736	γ = 89.09

Software Package:

Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MrBUMP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description