4JJP | pdb_00004jjp

2.06 Angstrom resolution crystal structure of phosphomethylpyrimidine kinase (thiD)from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb4JJP/pdb

• Classification: TRANSFERASE
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-03-08 Released: 2013-03-20 
• Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (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, 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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.9 kDa 
• Atom Count: 3,666 
• Modeled Residue Count: 448 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphomethylpyrimidine kinase	A, B	267	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_15990, thiD EC: 2.7.4.7 (PDB Primary Data), 2.7.1.49 (UniProt)
UniProt
Find proteins for Q186F5 (Clostridioides difficile (strain 630)) Explore Q186F5  Go to UniProtKB:  Q186F5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	C [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34jjp

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.751	α = 90
b = 79.741	β = 90
c = 92.863	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Halavaty, A.S., Wawrzak, Z., Onopriyenko, O., Grimshaw, S., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2026-04-01
  Changes: Database references, Structure summary