Download MendeleyThe crystal structure of a putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes
Fan, Y., Volkart, L., Clancy, S., Joachimiak, A.To be published.
3JRK | pdb_00003jrk
3JRK | pdb_00003jrk
A putative tagatose 1,6-diphosphate aldolase from Streptococcus pyogenes
- PDB DOI: https://doi.org/10.2210/pdb3JRK/pdb
- Classification: LYASE
- Organism(s): Streptococcus pyogenes serotype M1
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-09-08 Released: 2009-09-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.230 (Depositor), 0.238 (DCC)
- R-Value Work: 0.188 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.190 (Depositor)
wwPDB Validation 3D Report Full Report
This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecule Content
- Total Structure Weight: 291.57 kDa
- Atom Count: 21,833
- Modeled Residue Count: 2,572
- Deposited Residue Count: 2,576
- Unique protein chains: 1
Macromolecules
Find similar proteins by:
| 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Tagatose 1,6-diphosphate aldolase 2 | 322 | Streptococcus pyogenes serotype M1 | Mutation(s): 0 Gene Names: lacD.2, lacD2, M5005_Spy1635, SPy_1919 EC: 4.1.2.40 |  | |
UniProt | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P63705 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Download:Ideal Coordinates CCD File | I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B, C, D, E A, B, C, D, E, F, G, H | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.97 Å
- R-Value Free: 0.230 (Depositor), 0.238 (DCC)
- R-Value Work: 0.188 (Depositor), 0.200 (DCC)
- R-Value Observed: 0.190 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.517 | α = 90 |
| b = 169.729 | β = 94.09 |
| c = 167.054 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| SHELXD | phasing |
| MLPHARE | phasing |
| ARP | model building |
| WARP | model building |
| HKL-3000 | phasing |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-09-22 Deposition Author(s): Fan, Y., Volkart, L., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-09-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
