Download MendeleyCrystal 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.
3N0Q | pdb_00003n0q
3N0Q | pdb_00003n0q
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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.186 (Depositor), 0.136 (DCC)
- R-Value Work: 0.154 (Depositor)
- R-Value Observed: 0.156 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.5 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative aromatic-ring hydroxylating dioxygenase | 409 | Ruegeria sp. TM1040 | Mutation(s): 0 Gene Names: benA, TM1040_3219 |  | |
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| FES Download:Ideal Coordinates CCD File | B [auth A] | FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N |  | ||
| TRS Download:Ideal Coordinates CCD File | F [auth A], G [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | ||
| GOL Download:Ideal Coordinates CCD File | H [auth A], I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| NI Download:Ideal Coordinates CCD File | C [auth A], D [auth A] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |  | ||
| CL Download:Ideal Coordinates CCD File | E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on 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 (Depositor), 0.136 (DCC)
- R-Value Work: 0.154 (Depositor)
- R-Value Observed: 0.156 (Depositor)
Diffraction Data:
Space Group: P 63
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 97.533 | α = 90 |
| b = 97.533 | β = 90 |
| c = 96.522 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2010-06-09 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- 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
