Download MendeleyCrystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3R13
Crystal structure of a Deoxyribose-phosphate aldolase (TM_1559) from THERMOTOGA MARITIMA at 1.83 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3R13/pdb
- Classification: LYASE
- Organism(s): Thermotoga maritima
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-03-09 Released: 2011-03-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.193
- R-Value Work: 0.154
- R-Value Observed: 0.156
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 |
| Deoxyribose-phosphate aldolase | 260 | Thermotoga maritima | Mutation(s): 0 Gene Names: deoC, TM1559, TM_1559 EC: 4.1.2.4 |  | |
UniProt | |||||
Find proteins for Q9X1P5 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1P5 Go to UniProtKB: Q9X1P5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9X1P5 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | G [auth A], L [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| ACT Query on ACT | D [auth A] E [auth A] F [auth A] H [auth B] J [auth B] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
| UNL Query on UNL | C [auth A], I [auth B] | Unknown ligand QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| 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: 1.83 Å
- R-Value Free: 0.193
- R-Value Work: 0.154
- R-Value Observed: 0.156
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M33R13
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 53.904 | α = 90 |
| b = 52.481 | β = 95.59 |
| c = 85.462 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SHELX | phasing |
| SHARP | phasing |
| SCALA | data scaling |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| SHELXD | phasing |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2011-03-30 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2011-03-30
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2011-07-20
Changes: Data collection, Derived calculations, Non-polymer description, Other, Structure summary - Version 1.3: 2017-11-08
Changes: Refinement description - Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
