Download MendeleyCrystal structure of macrolide glycosyltransferases OleD
Olmos Jr., J.L., Martinez iii, E., Wang, F., Helmich, K.E., Singh, S., Xu, W., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N.To be published.
4M60 | pdb_00004m60
Crystal structure of macrolide glycosyltransferases OleD
- PDB DOI: https://doi.org/10.2210/pdb4M60/pdb
- Classification: TRANSFERASE
- Organism(s): Streptomyces antibioticus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2013-08-08 Released: 2013-09-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.77 Å
- R-Value Free: 0.208 (Depositor), 0.212 (DCC)
- R-Value Work: 0.183 (Depositor), 0.187 (DCC)
- R-Value Observed: 0.184 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Oleandomycin glycosyltransferase | 418 | Streptomyces antibioticus | Mutation(s): 0 Gene Names: oleD EC: 2.4.1 |  | |
UniProt | |||||
Find proteins for Q53685 (Streptomyces antibioticus) Explore Q53685 Go to UniProtKB: Q53685 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q53685 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | B [auth A] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| 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: 1.77 Å
- R-Value Free: 0.208 (Depositor), 0.212 (DCC)
- R-Value Work: 0.183 (Depositor), 0.187 (DCC)
- R-Value Observed: 0.184 (Depositor)
Space Group: H 3
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 124.134 | α = 90 |
| b = 124.134 | β = 90 |
| c = 67.636 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| HKL-2000 | data collection |
| HKL-2000 | data reduction |
| PHENIX | phasing |
| DENZO | data reduction |
Entry History
Deposition Data
- Released Date: 2013-09-04 Deposition Author(s): Olmos Jr., J.L., Martinez III, E., Wang, F., Helmich, K.E., Singh, S., Xu, W., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Revision History (Full details and data files)
- Version 1.0: 2013-09-04
Type: Initial release - Version 1.1: 2017-11-15
Changes: Refinement description - Version 1.2: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description - Version 1.3: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
