7PDA | pdb_00007pda

Crystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium fortuitum

• PDB DOI: https://doi.org/10.2210/pdb7PDA/pdb

• Classification: LYASE
• Organism(s): Mycolicibacterium fortuitum, unidentified
• Expression System: Escherichia, unidentified
• Mutation(s): No 


• Deposited: 2021-08-05 Released: 2022-08-24 
• Deposition Author(s): Gahloth, D., Leys, D.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Phenazine 1-carboxylic acid decarboxylase from Mycobacterium fortuitum

Gahloth, D., Leys, D.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B1C1D1E1F1G1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 53.24 kDa 
• Atom Count: 3,745 
• Modeled Residue Count: 482 
• Deposited Residue Count: 484 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UbiD family decarboxylase	A	479	Mycolicibacterium fortuitum	Mutation(s): 0  Gene Names: XA26_16650
UniProt
Find proteins for A0A0N9Y7U2 (Mycolicibacterium fortuitum) Explore A0A0N9Y7U2  Go to UniProtKB:  A0A0N9Y7U2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UNK	B	5	unidentified	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4LU (Subject of Investigation/LOI)	D [auth A]	1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol C22 H30 N4 O9 P KOUJZPGFPGLHCZ-IYOUNJFTSA-O
MN	C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 3 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.696	α = 90
b = 124.696	β = 90
c = 68.846	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Gahloth, D., Leys, D.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description