Macromolecule Content

Total Structure Weight: 109.03 kDa
Atom Count: 7997
Residue Count: 930
Unique protein chains: 1

4RIT

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

DOI: 10.2210/pdb4RIT/pdb

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

Deposited: 2014-10-07 Released: 2014-10-22
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.173
R-Value Work: 0.150
R-Value Observed: 0.151

wwPDB Validation 3D Report Full Report

Literature

The yellow 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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal-dependent decarboxylase	A, B	486	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0 Gene Names: Sthe_2364 EC: 4.1.1.15
Find proteins for D1C7D8 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022)) Explore D1C7D8 Go to UniProtKB: D1C7D8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain J [B] SDF format, chain K [B] SDF format, chain S [A] MOL2 format, chain J [B] MOL2 format, chain K [B] MOL2 format, chain S [A]	A, B	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [B] SDF format, chain F [B] SDF format, chain G [B] SDF format, chain H [B] SDF format, chain I [B] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain P [A] SDF format, chain Q [A] SDF format, chain R [A] MOL2 format, chain E [B] MOL2 format, chain F [B] MOL2 format, chain G [B] MOL2 format, chain H [B] MOL2 format, chain I [B] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain P [A] MOL2 format, chain Q [A] MOL2 format, chain R [A]	A, B	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [B] SDF format, chain D [B] SDF format, chain L [A] MOL2 format, chain C [B] MOL2 format, chain D [B] MOL2 format, chain L [A]	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.173
R-Value Work: 0.150
R-Value Observed: 0.151
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.483	α = 90
b = 118.566	β = 90
c = 126.018	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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2014-10-07
Released Date: 2014-10-22

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History

Version 1.0: 2014-10-22
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.