Download MendeleyCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
Abendroth, J., Davies, D.R., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
7SY9 | pdb_00007sy9
Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from Pseudomonas aeruginosa PAO1
- PDB DOI: https://doi.org/10.2210/pdb7SY9/pdb
- Classification: LIGASE
- Organism(s): Pseudomonas aeruginosa PAO1
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2021-11-24 Released: 2021-12-15
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.247 (Depositor), 0.240 (DCC)
- R-Value Work: 0.212 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.214 (Depositor)
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| UDP-N-acetylmuramoylalanine--D-glutamate ligase | 448 | Pseudomonas aeruginosa PAO1 | Mutation(s): 0 Gene Names: murD, PA4414 EC: 6.3.2.9 |  | |
UniProt | |||||
Find proteins for Q9HVZ9 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVZ9 Go to UniProtKB: Q9HVZ9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HVZ9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACT Query on ACT | C [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| FMT Query on FMT | D [auth A], E [auth B] | FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.75 Å
- R-Value Free: 0.247 (Depositor), 0.240 (DCC)
- R-Value Work: 0.212 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.214 (Depositor)
Diffraction Data: https://doi.org/10.18430/M37SY9
Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 94.75 | α = 90 |
| b = 94.75 | β = 90 |
| c = 442.92 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XDS | data reduction |
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
| Coot | model building |
| PHENIX | model building |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-12-15 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease, Seattle Structural Genomics Center for Infectious Disease (SSGCID)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | HHSN272201700059C |
Revision History (Full details and data files)
- Version 1.0: 2021-12-15
Type: Initial release - Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
