Download MendeleyStructural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum
Posner, M.G., Upadhyay, A., Crennell, S., Danson, M.J., Bagby, S.To be published.
3R07
Structural analysis of an archaeal lipoylation system. A bi-partite lipoate protein ligase and its E2 lipoyl domain from Thermoplasma acidophilum
- PDB DOI: https://doi.org/10.2210/pdb3R07/pdb
- Classification: TRANSFERASE
- Organism(s): Thermoplasma acidophilum DSM 1728
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2011-03-07 Released: 2012-04-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.254
- R-Value Work: 0.198
- R-Value Observed: 0.200
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Lipoate-protein ligase A subunit 1 | 285 | Thermoplasma acidophilum DSM 1728 | Mutation(s): 0 Gene Names: lplA, Ta0514 EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt) |  | |
UniProt | |||||
Find proteins for Q9HKT1 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKT1 Go to UniProtKB: Q9HKT1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HKT1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Putative lipoate-protein ligase A subunit 2 | B [auth C] | 91 | Thermoplasma acidophilum DSM 1728 | Mutation(s): 0 Gene Names: Ta0513, Ta0513m EC: 2.7.7.63 (PDB Primary Data), 6.3.1.20 (UniProt) |  |
UniProt | |||||
Find proteins for Q9HKT2 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)) Explore Q9HKT2 Go to UniProtKB: Q9HKT2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9HKT2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MPD Query on MPD | C [auth A], D [auth A] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| ACT Query on ACT | E [auth A], F [auth C] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.254
- R-Value Work: 0.198
- R-Value Observed: 0.200
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 118.57 | α = 90 |
| b = 118.57 | β = 90 |
| c = 72.92 | γ = 120 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| BALBES | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2012-04-25 Deposition Author(s): Posner, M.G., Upadhyay, U., Crennell, S.
Revision History (Full details and data files)
- Version 1.0: 2012-04-25
Type: Initial release - Version 1.1: 2012-05-23
Changes: Structure summary - Version 1.2: 2019-11-06
Changes: Advisory, Data collection, Database references - Version 1.3: 2023-09-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description
