4H3D | pdb_00004h3d

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 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

A high-throughput structural system biology approach to increase structure representation of proteins from Clostridioides difficile.

Rosas-Lemus, M., Dey, S., Minasov, G., Tan, K., Anderson, S.M., Brunzelle, J., Nocadello, S., Shabalin, I., Filippova, E., Halavaty, A., Kim, Y., Maltseva, N., Osipiuk, J., Minor, W., Joachimiak, A., Savchenko, A., Anderson, W.F., Satchell, K.J.F.

(2023) Microbiol Resour Announc 12: e0050723-e0050723

• PubMed: 37747257 
• DOI: https://doi.org/10.1128/MRA.00507-23
• Primary Citation Related Structures: 
  3SD7, 3SRT, 3UUW, 4DD5, 4DGT, 4DQ6, 4DUN, 4E1L, 4EGU, 4GIB, 4H3D, 4ISX, 4JJP, 4KD5, 4MFG, 4NMY, 4RN7, 5DZS, 5TTA, 5TV7, 5TXU, 6N7M, 6UE2, 6WY4, 7K1U, 7RL8, 7RLR


• PubMed Abstract: 
  

  Clostridioides difficile causes life-threatening gastrointestinal infections. It is a high-risk pathogen due to a lack of effective treatments, antimicrobial resistance, and a poorly conserved genomic core. Herein, we report 30 X-ray structures from a structure genomics pipeline spanning 13 years, representing 10.2% of the X-ray structures for this important pathogen.

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Organizational Affiliation: 
• Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
Center for Structural Biology of Infectious Diseases, Chicago, Illinois, USA.
Consortium for Advanced Science and Engineering, University of Chicago, Chicago, Illinois, USA.
Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, Illinois, USA.
Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA.
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA.
Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.

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 
• Modeled 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 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34h3d

Space Group: P 1 2₁ 1

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
• Version 1.4: 2024-11-27
  Changes: Structure summary
• Version 1.5: 2026-02-18
  Changes: Database references