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), 0.150 (DCC) 
• R-Value Work: 
  0.136 (Depositor), 0.130 (DCC) 
• R-Value Observed: 
  0.137 (Depositor) 

Literature

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

Anderson, S.M., Wawrzak, Z., Kudritska, M., Peterson, S.N., Anderson, W.F., Savchenko, A.

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 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), 0.150 (DCC) 
• R-Value Work:  0.136 (Depositor), 0.130 (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