4DUN

1.76A X-ray Crystal Structure of a Putative Phenazine Biosynthesis PhzC/PhzF Protein from Clostridium difficile (strain 630)

• PDB DOI: https://doi.org/10.2210/pdb4DUN/pdb

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


• Deposited: 2012-02-22 Released: 2012-03-14 
• Deposition Author(s): Brunzelle, J.S., Wawrzak, W., Kudritska, M., 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: 1.76 Å
• R-Value Free: 0.190 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

1.76A X-ray Crystal Structure of a Putative Phenazine Biosynthesis PhzC/PhzF Protein from Clostridium difficile (strain 630)

Brunzelle, J.S., Wawrzak, W., Kudritska, M., Anderson, W.F., Savchenko, A., 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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.08 kDa 
• Atom Count: 2,559 
• Modelled Residue Count: 259 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phenazine biosynthesis PhzC/PhzF protein	A	263	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD1761, CD630_17610
UniProt
Find proteins for Q186X0 (Clostridioides difficile (strain 630)) Explore Q186X0  Go to UniProtKB:  Q186X0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	C [auth A], E [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NI	D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.190 
• R-Value Work: 0.158 
• R-Value Observed: 0.158 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/m34dun

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.65	α = 90
b = 63.65	β = 90
c = 135.12	γ = 120

Software Package:

Software Name	Purpose
BLU-MAX	data collection
PHASER	phasing
PHENIX	model building
BUSTER	refinement
XDS	data reduction
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Brunzelle, J.S., Wawrzak, W., Kudritska, M., Anderson, W.F., Savchenko, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description