4RLG | pdb_00004rlg

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.162 (Depositor), 0.165 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 216.9 kDa
Atom Count: 15,766
Modeled Residue Count: 1,881
Deposited Residue Count: 1,944
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D1C7D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 A] SDF format, chain H [auth B] SDF format, chain L [auth D] SDF format, chain Q [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth D] MOL2 format, chain Q [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth D] mmCIF format, chain Q [auth C]	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		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain Q [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain L [auth D] Focus chain Q [auth C]
ABU Query on ABU Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	M [auth D], N [auth D]	GAMMA-AMINO-BUTANOIC ACID C₄ H₉ N O₂ BTCSSZJGUNDROE-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain M [auth D] Focus chain N [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth D] SDF format, chain R [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth D] MOL2 format, chain R [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain O [auth D] mmCIF format, chain R [auth C]	F [auth A], I [auth B], J [auth B], O [auth D], R [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain O [auth D] Focus chain R [auth C]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth D] SDF format, chain S [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth D] MOL2 format, chain S [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth D] mmCIF format, chain S [auth C]	G [auth A], K [auth B], P [auth D], S [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D] Focus chain S [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth D] Focus chain S [auth C]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C [auth D], D [auth C]	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on 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 (Depositor), 0.192 (DCC)
R-Value Work: 0.162 (Depositor), 0.165 (DCC)
R-Value Observed: 0.164 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

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 (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Database references, Derived calculations
Version 2.1: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary