Download MendeleyStructure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP
Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.To be published.
3LGX | pdb_00003lgx
Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP
- PDB DOI: https://doi.org/10.2210/pdb3LGX/pdb
- Classification: ATP binding protein
- Organism(s): Streptococcus pyogenes M1 GAS
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2010-01-21 Released: 2010-03-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.276 (Depositor), 0.270 (DCC)
- R-Value Work: 0.218 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.221 (Depositor)
Starting Model: experimental
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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 |
| D-alanine--poly(phosphoribitol) ligase subunit 1 | 521 | Streptococcus pyogenes M1 GAS | Mutation(s): 0 Gene Names: dltA, M5005_Spy1073, SPy_1312 EC: 6.1.1.13 (PDB Primary Data), 6.2.1.54 (UniProt) |  | |
UniProt | |||||
Find proteins for Q99ZA6 (Streptococcus pyogenes serotype M1) Explore Q99ZA6 Go to UniProtKB: Q99ZA6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q99ZA6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ATP Query on ATP | E [auth A], F [auth B], G [auth C], H [auth D] | ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.276 (Depositor), 0.270 (DCC)
- R-Value Work: 0.218 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.221 (Depositor)
Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 174.41 | α = 90 |
| b = 174.41 | β = 90 |
| c = 176.065 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| ADSC | data collection |
| HKL-2000 | data reduction |
| MOLREP | phasing |
Entry History
Deposition Data
- Released Date: 2010-03-02 Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)
Revision History (Full details and data files)
- Version 1.0: 2010-03-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary - Version 1.4: 2023-09-06
Changes: Data collection, Database references, Refinement description
