7CNT | pdb_00007cnt

Structure of 2,5-dihydroxypridine Dioxygenase from Pseudomonas putida KT2440 in complex with product N-formylmaleamic acid formed via in crystallo reaction with 2,5-dihydroxypridine

• PDB DOI: https://doi.org/10.2210/pdb7CNT/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-08-03 Released: 2020-12-16 
• Deposition Author(s): Liu, G.Q., Tang, H.Z.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

2,5-dihydroxypridine Dioxygenase in complex with 2,5-dihydroxypridine and product N-formylmaleamic acid

Liu, G.Q., Tang, H.Z.

(2020) Nat Commun 

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 247.25 kDa 
• Atom Count: 16,612 
• Modeled Residue Count: 2,088 
• Deposited Residue Count: 2,178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2,5-dihydroxypyridine 5,6-dioxygenase	A, B, C, D, E, F	363	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: nicX, PP_3945 EC: 1.13.11.9
UniProt
Find proteins for Q88FY1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88FY1  Go to UniProtKB:  Q88FY1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE2 (Subject of Investigation/LOI)	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.885	α = 90
b = 125.916	β = 90
c = 144.129	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-12-16 
Deposition Author(s): Liu, G.Q., Tang, H.Z.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2020-12-16
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Database references, Structure summary