Download MendeleyBiochemical and structural insights of Fe(II)/alpha-ketoglutarate/O2-dependent dioxygenase, KdoO from Methylacidiphilum infernorum V4
Chung, H.S., Pemble IV, C.W., Joo, S.H.To be published.
5Y9I
Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with Co(II)
- PDB DOI: https://doi.org/10.2210/pdb5Y9I/pdb
- Classification: BIOSYNTHETIC PROTEIN
- Organism(s): Methylacidiphilum infernorum V4
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2017-08-25 Released: 2018-10-31
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.195
- R-Value Work: 0.151
- R-Value Observed: 0.154
This is version 1.2 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 |
| Uncharacterized protein KdoO | 318 | Methylacidiphilum infernorum V4 | Mutation(s): 0 Gene Names: Minf_1012 |  | |
UniProt | |||||
Find proteins for B3DUR4 (Methylacidiphilum infernorum (isolate V4)) Explore B3DUR4 Go to UniProtKB: B3DUR4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B3DUR4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| BOG Query on BOG | D [auth A] | octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N |  | ||
| SO4 Query on SO4 | B [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ACT Query on ACT | H [auth A], I [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CO Query on CO | C [auth A] | COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A], F [auth A], G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.90 Å
- R-Value Free: 0.195
- R-Value Work: 0.151
- R-Value Observed: 0.154
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 46.263 | α = 90 |
| b = 59.566 | β = 90 |
| c = 116.95 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
| SHELXCD | phasing |
Entry History
Deposition Data
- Released Date: 2018-10-31 Deposition Author(s): Chung, H.S., Pemble, C.W., Joo, S.H.
Revision History (Full details and data files)
- Version 1.0: 2018-10-31
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.2: 2024-03-27
Changes: Data collection, Database references, Structure summary
