3N0Q

Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from SILICIBACTER SP. TM1040 at 1.80 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3N0Q/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Ruegeria sp. TM1040
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-14 Released: 2010-06-09 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.186 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from SILICIBACTER SP. TM1040 at 1.80 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration, light scattering

Macromolecule Content

• Total Structure Weight: 47.25 kDa 
• Atom Count: 3,823 
• Modelled Residue Count: 402 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aromatic-ring hydroxylating dioxygenase	A	409	Ruegeria sp. TM1040	Mutation(s): 0  Gene Names: benA, TM1040_3219
UniProt
Find proteins for Q1GMC3 (Ruegeria sp. (strain TM1040)) Explore Q1GMC3  Go to UniProtKB:  Q1GMC3

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FES	B [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
TRS	F [auth A], G [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	C [auth A], D [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	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: 0.186 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 6₃
• Diffraction Data: https://doi.org/10.18430/M33N0Q

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.533	α = 90
b = 97.533	β = 90
c = 96.522	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-09 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-06-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary