4RJ0 | pdb_00004rj0

The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745

• PDB DOI: https://doi.org/10.2210/pdb4RJ0/pdb

• Classification: LYASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-10-07 Released: 2014-11-12 
• Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.193 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.168 (Depositor) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of Y333N mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus dsm 20745

Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 212.89 kDa 
• Atom Count: 15,125 
• Modeled Residue Count: 1,869 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal-dependent decarboxylase	A [auth B], B [auth A], C, D	486	Sphaerobacter thermophilus DSM 20745	Mutation(s): 1  Gene Names: Sthe_2364 EC: 4.1.1.15
UniProt
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C7D8  Go to UniProtKB:  D1C7D8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	H [auth D]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
PO4	G [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	E [auth A], F [auth A], I [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A [auth B], B [auth A], C, D	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.193 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.168 (Depositor) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.984	α = 90
b = 124.198	β = 99.56
c = 129.942	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-12 
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-11-12
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection