4EGU | pdb_00004egu

0.95A Resolution Structure of a Histidine Triad Protein from Clostridium difficile

• PDB DOI: https://doi.org/10.2210/pdb4EGU/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Clostridioides difficile 630
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-01 Released: 2012-04-18 
• Deposition Author(s): Anderson, S.M., Wawrzak, Z., Kudritska, M., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free: 
  0.152 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.92 kDa 
• Atom Count: 2,381 
• Modeled Residue Count: 233 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
histidine triad (HIT) protein	A, B	119	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD630_24470
UniProt
Find proteins for Q182D4 (Clostridioides difficile (strain 630)) Explore Q182D4  Go to UniProtKB:  Q182D4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	C [auth A], F [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.95 Å
• R-Value Free:  0.152 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.137 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34egu

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.065	α = 90
b = 65.848	β = 90
c = 89.041	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-18 
Deposition Author(s): Anderson, S.M., Wawrzak, Z., Kudritska, M., Peterson, S.N., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-04-18
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2026-04-29
  Changes: Database references, Structure summary