4RLG

The clear crystal structure of pyridoxal-dependent decarboxylase from sphaerobacter thermophilus dsm 20745

• PDB DOI: https://doi.org/10.2210/pdb4RLG/pdb

• Classification: LYASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-16 Released: 2014-10-29 
• 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: 1.90 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

The clear crystal structure of 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: 216.9 kDa 
• Atom Count: 15,766 
• Modelled Residue Count: 1,881 
• Deposited Residue Count: 1,944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal-dependent decarboxylase	A, B, C [auth D], D [auth C]	486	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	E [auth A], H [auth B], L [auth D], Q [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
ABU	M [auth D], N [auth D]	GAMMA-AMINO-BUTANOIC ACID C4 H9 N O2 BTCSSZJGUNDROE-UHFFFAOYSA-N
GOL	F [auth A], I [auth B], J [auth B], O [auth D], R [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	G [auth A], K [auth B], P [auth D], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A, B, C [auth D], D [auth C]	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A, B, C [auth D], D [auth C]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.191 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.32	α = 90
b = 124.981	β = 99.49
c = 132.76	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: 2014-10-29 
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations