Download MendeleyD-alanine--D-alanine ligase from Yersinia pestis.
Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A.To be published.
3V4Z
D-alanine--D-alanine ligase from Yersinia pestis
- PDB DOI: https://doi.org/10.2210/pdb3V4Z/pdb
- Classification: LIGASE
- Organism(s): Yersinia pestis CO92
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-12-15 Released: 2011-12-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.289
- R-Value Work: 0.205
- R-Value Observed: 0.209
wwPDB Validation 3D Report Full Report
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 |
| D-alanine--D-alanine ligase | 309 | Yersinia pestis CO92 | Mutation(s): 0 Gene Names: ddl, ddlB, y3624, YPO0557, YP_3627 EC: 6.3.2.4 |  | |
UniProt | |||||
Find proteins for Q8ZIE7 (Yersinia pestis) Explore Q8ZIE7 Go to UniProtKB: Q8ZIE7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8ZIE7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PGE Query on PGE | D [auth B] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | C [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.69 Å
- R-Value Free: 0.289
- R-Value Work: 0.205
- R-Value Observed: 0.209
- Space Group: P 31 2 1
- Diffraction Data: https://doi.org/10.18430/M33V4Z
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 100.637 | α = 90 |
| b = 100.637 | β = 90 |
| c = 110.304 | γ = 120 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MOLREP | phasing |
| HKL-3000 | phasing |
Entry History
Deposition Data
- Released Date: 2011-12-28 Deposition Author(s): Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2011-12-28
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
