Download MendeleyCrystal structure of putative pyridoxal 5'-phosphate-dependent C-S lyase (YP_813084.1) from LACTOBACILLUS DELBRUECKII BULGARICUS ATCC BAA-365 at 1.61 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3DZZ
CRYSTAL STRUCTURE OF A PUTATIVE PLP-DEPENDENT AMINOTRANSFERASE (LBUL_1103) FROM LACTOBACILLUS DELBRUECKII SUBSP. AT 1.61 A RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb3DZZ/pdb
- Classification: TRANSFERASE
- Organism(s): Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-07-30 Released: 2008-08-12
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.61 Å
- R-Value Free: 0.175
- R-Value Work: 0.144
- R-Value Observed: 0.146
wwPDB Validation 3D Report Full Report
This is version 1.4 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 |
| putative pyridoxal 5'-phosphate-dependent C-S lyase | 391 | Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 | Mutation(s): 0 Gene Names: YP_813084.1, LBUL_1103 |  | |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PG4 Query on PG4 | L [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| PEG Query on PEG | G [auth A], H [auth A], I [auth A], M [auth B], N [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | F [auth A], K [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| CA Query on CA | C [auth A], D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| LLP Query on LLP | A, B | L-PEPTIDE LINKING | C14 H22 N3 O7 P |  | LYS |
| 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: 1.61 Å
- R-Value Free: 0.175
- R-Value Work: 0.144
- R-Value Observed: 0.146
- Space Group: C 1 2 1
- Diffraction Data: https://doi.org/10.18430/M33DZZ
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 115.8 | α = 90 |
| b = 94.8 | β = 127.13 |
| c = 84.602 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2008-08-12 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2008-08-12
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
