Download MendeleyCrystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone (to be published)
Wang, F., Johnson, B.R., Huber, T.D., Singh, S., Thorson, J.S., Phillips Jr., G.N.To be published.
5JR3
Crystal structure of carminomycin-4-O-methyltransferase DnrK in complex with SAH and 4-methylumbelliferone
- PDB DOI: https://doi.org/10.2210/pdb5JR3/pdb
- Classification: TRANSFERASE
- Organism(s): Streptomyces peucetius
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-05-05 Released: 2016-06-01
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.180
- R-Value Work: 0.160
- R-Value Observed: 0.160
This is version 2.1 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 |
| Carminomycin 4-O-methyltransferase DnrK | 376 | Streptomyces peucetius | Mutation(s): 0 Gene Names: dnrK EC: 2.1.1.292 |  | |
UniProt | |||||
Find proteins for Q06528 (Streptomyces peucetius) Explore Q06528 Go to UniProtKB: Q06528 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q06528 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SAH Query on SAH | D [auth A], J [auth B], R [auth C] | S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N |  | ||
| 4MU Query on 4MU | E [auth A], K [auth B], S [auth C] | 7-hydroxy-4-methyl-2H-chromen-2-one C10 H8 O3 HSHNITRMYYLLCV-UHFFFAOYSA-N |  | ||
| SO4 Query on SO4 | F [auth A] G [auth A] H [auth A] I [auth A] L [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.180
- R-Value Work: 0.160
- R-Value Observed: 0.160
- Space Group: C 1 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 122.16 | α = 90 |
| b = 111.098 | β = 120.02 |
| c = 116.225 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-06-01 Deposition Author(s): Wang, F., Johnson, B.R., Huber, T.D., Singh, S., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | U01GM098248 |
Revision History (Full details and data files)
- Version 1.0: 2016-06-01
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2019-12-25
Changes: Author supporting evidence - Version 2.0: 2023-03-22
Changes: Advisory, Atomic model, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary - Version 2.1: 2023-10-25
Changes: Data collection, Refinement description
