Download MendeleyCrystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
2P8I
Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia xenovorans LB400 at 1.40 A resolution
- PDB DOI: https://doi.org/10.2210/pdb2P8I/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Paraburkholderia xenovorans LB400
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2007-03-22 Released: 2007-04-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.173
- R-Value Work: 0.144
- R-Value Observed: 0.145
wwPDB Validation 3D Report Full Report
This is version 1.6 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 |
| Putative dioxygenase | 117 | Paraburkholderia xenovorans LB400 | Mutation(s): 2 Gene Names: YP_555069.1, Bxeno_B2751, Bxe_B0224 |  | |
UniProt | |||||
Find proteins for Q13JM0 (Paraburkholderia xenovorans (strain LB400)) Explore Q13JM0 Go to UniProtKB: Q13JM0 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q13JM0 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | M [auth C] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | Ligand Interaction | |
| PO4 Query on PO4 | F [auth A], K [auth B], L [auth C], Q [auth D] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | Ligand Interaction | |
| EDO Query on EDO | G [auth A], H [auth A], N [auth C], O [auth C], R [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | E [auth A], I [auth B], J [auth B], P [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.40 Å
- R-Value Free: 0.173
- R-Value Work: 0.144
- R-Value Observed: 0.145
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M32P8I
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 43.835 | α = 90 |
| b = 138.772 | β = 98.43 |
| c = 44.046 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| REFMAC | refinement |
| SCALA | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| MOSFLM | data reduction |
| CCP4 | data scaling |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2007-04-24 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-04-24
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2017-10-25
Changes: Author supporting evidence - Version 1.5: 2023-01-25
Changes: Database references, Derived calculations - Version 1.6: 2023-09-20
Changes: Data collection, Refinement description
