4DQ6

Crystal structure of PLP-bound putative aminotransferase from Clostridium difficile 630

• PDB DOI: https://doi.org/10.2210/pdb4DQ6/pdb

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


• Deposited: 2012-02-15 Released: 2012-02-29 
• Deposition Author(s): Shabalin, I.G., Onopriyenko, O., Kudritska, M., Chruszcz, M., Grimshaw, S., Porebski, P.J., Cooper, D.R., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Crystal structures of putative aminotransferase from Clostridium difficile 630

Shabalin, I.G., Onopriyenko, O., Kudritska, M., Grimshaw, S., Chruszcz, M., Porebski, P.J., Cooper, D.R., Savchenko, A., Anderson, W.F., Minor, W.

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: 90.77 kDa 
• Atom Count: 7,410 
• Modelled Residue Count: 776 
• Deposited Residue Count: 782 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative pyridoxal phosphate-dependent transferase	A, B	391	Clostridioides difficile 630	Mutation(s): 0  Gene Names: CD2733, CD630_27330 EC: 4.4.1.13
UniProt
Find proteins for Q183G9 (Clostridioides difficile (strain 630)) Explore Q183G9  Go to UniProtKB:  Q183G9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
CL	D [auth A], E [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.186 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 1 2₁ 1
• Diffraction Data: https://doi.org/10.18430/M34DQ6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.426	α = 90
b = 56.094	β = 99.33
c = 85.275	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Shabalin, I.G., Onopriyenko, O., Kudritska, M., Chruszcz, M., Grimshaw, S., Porebski, P.J., Cooper, D.R., Savchenko, A., Anderson, W.F., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2022-04-13
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-09-13
  Changes: Data collection, Refinement description