Download MendeleyCrystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
Bolejack, M.J., Davies, D.R., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
6VJU
Crystal Structure of Cystathionine beta synthase from Legionella pneumophila with LLP, PLP, and homocysteine
- PDB DOI: https://doi.org/10.2210/pdb6VJU/pdb
- Classification: LYASE
- Organism(s): Legionella pneumophila
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-01-17 Released: 2020-02-05
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.180
- R-Value Work: 0.148
- R-Value Observed: 0.149
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 |
| Cystathionine beta-lyase | 324 | Legionella pneumophila | Mutation(s): 0 Gene Names: C3927_14920, DI056_06925, DI105_06930 |  | |
UniProt | |||||
Find proteins for Q5ZRD1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRD1 Go to UniProtKB: Q5ZRD1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5ZRD1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cystathionine beta-lyase | 324 | Legionella pneumophila | Mutation(s): 0 Gene Names: C3927_14920, DI056_06925, DI105_06930 |  | |
UniProt | |||||
Find proteins for Q5ZRD1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRD1 Go to UniProtKB: Q5ZRD1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q5ZRD1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Query on PLP | S [auth B] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| HCS Query on HCS | K [auth A] | 2-AMINO-4-MERCAPTO-BUTYRIC ACID C4 H9 N O2 S FFFHZYDWPBMWHY-VKHMYHEASA-N |  | ||
| EDO Query on EDO | C [auth A] D [auth A] E [auth A] H [auth A] M [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A] G [auth A] I [auth A] J [auth A] L [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.30 Å
- R-Value Free: 0.180
- R-Value Work: 0.148
- R-Value Observed: 0.149
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.35 | α = 90 |
| b = 91.79 | β = 90 |
| c = 93.77 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
Entry History
Deposition Data
- Released Date: 2020-02-05 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2020-02-05
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description - Version 1.2: 2023-11-15
Changes: Data collection - Version 1.3: 2024-04-03
Changes: Structure summary
