Download MendeleyCrystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3EBY
Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3EBY/pdb
- Classification: structural genomics, unknown function
- Organism(s): Novosphingobium aromaticivorans DSM 12444
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-08-28 Released: 2008-09-09
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.75 Å
- R-Value Free: 0.205
- R-Value Work: 0.168
- R-Value Observed: 0.170
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| beta subunit of a putative Aromatic-ring-hydroxylating dioxygenase | 163 | Novosphingobium aromaticivorans DSM 12444 | Mutation(s): 0 Gene Names: YP_001165631.1, Saro_3860 |  | |
UniProt | |||||
Find proteins for A4XDU4 (Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)) Explore A4XDU4 Go to UniProtKB: A4XDU4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A4XDU4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CL Query on CL | B [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: 1.75 Å
- R-Value Free: 0.205
- R-Value Work: 0.168
- R-Value Observed: 0.170
- Space Group: H 3 2
- Diffraction Data: https://doi.org/10.18430/M33EBY
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.29 | α = 90 |
| b = 80.29 | β = 90 |
| c = 145.02 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-09-09 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-09-09
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
