4H3D

1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.

• PDB DOI: https://doi.org/10.2210/pdb4H3D/pdb

• Classification: LYASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-09-13 Released: 2012-09-26 
• Deposition Author(s): Minasov, G., Light, S.H., Shuvalova, L., Duban, M.-E., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.199 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

1.95 Angstrom Crystal Structure of of Type I 3-Dehydroquinate Dehydratase (aroD) from Clostridium difficile with Covalent Modified Comenic Acid.

Minasov, G., Light, S.H., Shuvalova, L., Duban, M.-E., Dubrovska, I., Winsor, J., Papazisi, L., 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 assigned by authors.

Macromolecule Content

• Total Structure Weight: 118.12 kDa 
• Atom Count: 9,339 
• Modelled Residue Count: 1,011 
• Deposited Residue Count: 1,032 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D	258	Clostridioides difficile 630	Mutation(s): 0  Gene Names: aroD, CD630_22170 EC: 4.2.1.10
UniProt
Find proteins for Q186A6 (Clostridioides difficile (strain 630)) Explore Q186A6  Go to UniProtKB:  Q186A6

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SHL	G [auth A], I [auth B], L [auth C], M [auth D]	5-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxylic acid C7 H6 O5 ANRPPKUCFMTTIH-UHFFFAOYSA-N
PGE	E [auth A], K [auth C]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	F [auth A], H [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	J [auth B], N [auth D], O [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.199 
• R-Value Work: 0.156 
• R-Value Observed: 0.158 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/m34h3d

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.275	α = 90
b = 138.688	β = 90.01
c = 66.315	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-26 
Deposition Author(s): Minasov, G., Light, S.H., Shuvalova, L., Duban, M.-E., Dubrovska, I., Winsor, J., Papazisi, L., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-09-26
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description