Download MendeleyThe crystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant
Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.To be published.
5D5S
Crystal structure of methionine gamma-lyase from Citrobacter freundii, S339A mutant
- PDB DOI: https://doi.org/10.2210/pdb5D5S/pdb
- Classification: LYASE
- Organism(s): Citrobacter freundii
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2015-08-11 Released: 2016-08-17
- Funding Organization(s): RFBR
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 ?
- R-Value Free: 0.205
- R-Value Work: 0.173
- R-Value Observed: 0.174
Starting Model: experimental
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This is version 2.0 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 |
| Methionine gamma-lyase | 398 | Citrobacter freundii | Mutation(s): 1 Gene Names: TN42_08855, TO64_18625 EC: 4.4.1.11 |  | |
UniProt | |||||
Find proteins for A0A0A5P8W7 (Citrobacter freundii) Explore A0A0A5P8W7 Go to UniProtKB: A0A0A5P8W7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A0A5P8W7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PLP Query on PLP | D [auth A] | PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | B [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSO Query on CSO | A | L-PEPTIDE LINKING | C3 H7 N O3 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 ?
- R-Value Free: 0.205
- R-Value Work: 0.173
- R-Value Observed: 0.174
- Space Group: I 2 2 2
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 56.659 | ¦Á = 90 |
| b = 123.09 | ¦Â = 90 |
| c = 128.785 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| MxCuBE | data collection |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-08-17 Deposition Author(s): Revtovich, S.V., Nikulin, A.D., Anufrieva, N.V., Morozova, E.A., Demidkina, T.V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| RFBR | Russian Federation | -- |
Revision History (Full details and data files)
- Version 1.0: 2016-08-17
Type: Initial release - Version 2.0: 2024-01-10
Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description
