Download MendeleyStructure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cefapirin
Filippova, E.V., Minasov, G., Kiryukhina, O., Clancy, S., Joachimiak, A., Anderson, W.F.To be published.
4R3J
Structure of a putative peptidoglycan glycosyltransferase from Atopobium parvulum in complex with cefapirin
- PDB DOI: https://doi.org/10.2210/pdb4R3J/pdb
- Classification: TRANSFERASE
- Organism(s): Lancefieldella parvula DSM 20469
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2014-08-15 Released: 2014-09-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.44 Å
- R-Value Free: 0.231
- R-Value Work: 0.171
- R-Value Observed: 0.174
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 | |
| CFU Query on CFU | C [auth A], G [auth B] | (2R)-2-[(1R)-1-(acetylamino)-2-oxoethyl]-5-methyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid C10 H14 N2 O4 S POOBXVPMJBGTRO-VXNVDRBHSA-N |  | ||
| PO4 Query on PO4 | E [auth A], F [auth A], J [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| GOL Query on GOL | D [auth A], H [auth B], I [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-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: 2.44 Å
- R-Value Free: 0.231
- R-Value Work: 0.171
- R-Value Observed: 0.174
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 99.633 | α = 90 |
| b = 119.836 | β = 90 |
| c = 82.544 | 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 - Version 1.3: 2023-12-06
Changes: Data collection
