4RM1

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus DSM 20745

PDB DOI: https://doi.org/10.2210/pdb4RM1/pdb

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

Deposited: 2014-10-18 Released: 2014-11-12
Deposition Author(s): Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.99 Å
R-Value Free: 0.203
R-Value Work: 0.169
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The crystal structure of Y333Q mutant pyridoxal-dependent decarboxylase from Sphaerobacter thermophilus DSM 20745

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

To be published.

Macromolecule Content

Total Structure Weight: 213.44 kDa
Atom Count: 15,734
Modelled Residue Count: 1,893
Deposited Residue Count: 1,944
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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 DSM 20745 / S 6022)) Explore D1C7D8 Go to UniProtKB: D1C7D8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1C7D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PMP Query on PMP Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain M [auth C] MOL2 format, chain E [auth B] MOL2 format, chain M [auth C]	E [auth B], M [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C₈ H₁₃ N₂ O₅ P ZMJGSOSNSPKHNH-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth B] Focus chain M [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A]	F [auth B] G [auth B] H [auth B] J [auth A] K [auth A] F [auth B], G [auth B], H [auth B], J [auth A], K [auth A], L [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain N [auth D] MOL2 format, chain I [auth B] MOL2 format, chain N [auth D]	I [auth B], N [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth B] Focus chain N [auth D] Interactions & Density Focus chain I [auth B] Focus chain N [auth D]