Download MendeleyCrystal Structure of a TenA Homolog/Thi-4 Thiaminase from Pyrobaculum Aerophilum
Sawaya, M.R., Chan, S., Han, G.W., Pashkov, I., Perry, L.J., Yeates, T.O.To be published.
2GM8 | pdb_00002gm8
TenA Homolog/Thi-4 Thiaminase complexed with product 4-amino-5-hydroxymethyl-2-methylpyrimidine
- PDB DOI: https://doi.org/10.2210/pdb2GM8/pdb
- Classification: TRANSFERASE
- Organism(s): Pyrobaculum aerophilum str. IM2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2006-04-06 Released: 2006-04-18
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.187 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.189 (Depositor)
Starting Model: experimental
View more details
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 |
| tenA homolog/Thi-4 Thiaminase | 221 | Pyrobaculum aerophilum str. IM2 | Mutation(s): 0 Gene Names: tenA/thi4 (pag5_170) EC: 2.5.1.2 |  | |
UniProt | |||||
Find proteins for Q8ZZM9 (Pyrobaculum aerophilum (strain ATCC 51768 / DSM 7523 / JCM 9630 / CIP 104966 / NBRC 100827 / IM2)) Explore Q8ZZM9 Go to UniProtKB: Q8ZZM9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8ZZM9 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HMH Query on HMH | E [auth A], G [auth B], H [auth C], I [auth D] | 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE C6 H9 N3 O VUTBELPREDJDDH-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | F [auth A], J [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.50 Å
- R-Value Free: 0.237 (Depositor), 0.240 (DCC)
- R-Value Work: 0.187 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.189 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 70.647 | α = 90 |
| b = 94.287 | β = 113.65 |
| c = 73.198 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| Blu-Ice | data collection |
Entry History
Deposition Data
- Released Date: 2006-04-18 Deposition Author(s): Sawaya, M.R., Chan, S., Han, G.W., Perry, L.J., Pashkov, I.
Revision History (Full details and data files)
- Version 1.0: 2006-04-18
Type: Initial release - Version 1.1: 2008-05-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance - Version 1.3: 2017-10-18
Changes: Refinement description - Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description
