Download MendeleyStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin
Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F.To be published.
4R23
Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with dicloxacillin
- PDB DOI: https://doi.org/10.2210/pdb4R23/pdb
- Classification: TRANSFERASE/TRANSFERASE INHIBITOR
- Organism(s): Lancefieldella parvula DSM 20469
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-08-08 Released: 2014-09-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.192
- R-Value Work: 0.155
- R-Value Observed: 0.157
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 |
| Peptidoglycan glycosyltransferase | 482 | Lancefieldella parvula DSM 20469 | Mutation(s): 0 Gene Names: Apar_1344 EC: 2.4.1.129 |  | |
UniProt | |||||
Find proteins for C8W8H7 (Lancefieldella parvula (strain ATCC 33793 / DSM 20469 / CCUG 32760 / JCM 10300 / KCTC 3663 / VPI 0546 / 1246)) Explore C8W8H7 Go to UniProtKB: C8W8H7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C8W8H7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| DXU Query on DXU | C [auth A], J [auth B] | (3R,4R,5R)-3-(2,6-dichlorophenyl)-N-{(1R)-1-[(2R,4S)-4-(dihydroxymethyl)-5,5-dimethyl-1,3-thiazolidin-2-yl]-2-oxoethyl}
-5-methyl-1,2-oxazolidine-4-carboxamide C19 H25 Cl2 N3 O5 S AXRWQAUUTZEPPM-YSIYDJFASA-N |  | ||
| P4G Query on P4G | D [auth A], E [auth A], F [auth A], K [auth B] | 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | G [auth A], H [auth A], I [auth A], L [auth B], M [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.84 Å
- R-Value Free: 0.192
- R-Value Work: 0.155
- R-Value Observed: 0.157
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.611 | α = 90 |
| b = 69.882 | β = 96.87 |
| c = 114.251 | γ = 90 |
| Software Name | Purpose |
|---|---|
| Blu-Ice | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2014-09-17 Deposition Author(s): Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-09-17
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary - Version 1.3: 2023-12-06
Changes: Data collection
