3N9T | pdb_00003n9t

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

• PDB DOI: https://doi.org/10.2210/pdb3N9T/pdb

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


• Deposited: 2010-05-31 Released: 2010-08-04 
• Deposition Author(s): Liu, W., Shen, W., Fang, P., Li, J., Cui, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Cryatal structure of Hydroxyquinol 1,2-dioxygenase from Pseudomonas putida DLL-E4

Liu, W., Shen, W., Fang, P., Li, J., Cui, Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 33.44 kDa 
• Atom Count: 2,418 
• Modeled Residue Count: 286 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PnpC	A	290	Pseudomonas putida	Mutation(s): 0  Gene Names: pnpC EC: 1.13.11.37
UniProt
Find proteins for C6FI44 (Pseudomonas putida) Explore C6FI44  Go to UniProtKB:  C6FI44

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGX	B [auth A]	1-HEPTADECANOYL-2-TRIDECANOYL-3-GLYCEROL-PHOSPHONYL CHOLINE C38 H77 N O8 P AZEAMUNCULVBPK-PSXMRANNSA-O
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
FE	D [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.362	α = 90
b = 38.933	β = 118.35
c = 82.476	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-04 
Deposition Author(s): Liu, W., Shen, W., Fang, P., Li, J., Cui, Z.

Revision History  

• Version 1.0: 2010-08-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Experimental preparation
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description