4RIT | pdb_00004rit

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

PDB DOI: https://doi.org/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 (Depositor), 0.176 (DCC)
R-Value Work:
0.150 (Depositor), 0.158 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 109.03 kDa
Atom Count: 7,997
Modeled Residue Count: 930
Deposited Residue Count: 972
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal-dependent decarboxylase	A [auth B], B [auth A]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D1C7D8
Sequence Annotations 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 [auth B] SDF format, chain S [auth A] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain S [auth A] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain S [auth A] mmCIF format, chain K [auth B]	J [auth B], K [auth B], S [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain S [auth A] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain S [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain N [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain N [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] G [auth B] H [auth B] I [auth B] E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain L [auth A] SDF format, chain C [auth B] MOL2 format, chain D [auth B] MOL2 format, chain L [auth A] MOL2 format, chain C [auth B] mmCIF format, chain D [auth B] mmCIF format, chain L [auth A] mmCIF format, chain C [auth B]	C [auth B], D [auth B], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth B] Focus chain D [auth B] Focus chain L [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth B] Focus chain L [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A [auth B], B [auth A]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A [auth B], B [auth A]	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 (Depositor), 0.176 (DCC)
R-Value Work: 0.150 (Depositor), 0.158 (DCC)
R-Value Observed: 0.151 (Depositor)

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-10-22

Deposition Author(s):

Wu, R.

Clancy, S.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-10-22
Type: Initial release
Version 1.1: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary