Download MendeleyThe crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482
Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A.To be published.
5C0P
The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482
- PDB DOI: 10.2210/pdb5C0P/pdb
- Classification: HYDROLASE
- Organism(s): Bacteroides thetaiotaomicron VPI-5482
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2015-06-12 Released: 2015-07-01
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.164
- R-Value Work: 0.149
- R-Value Observed: 0.150
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Endo-arabinase | A | 298 | Bacteroides thetaiotaomicron VPI-5482 | Mutation(s): 0 Gene Names: BT_1873 |  |
UniProt | |||||
Find proteins for Q8A6K8 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A6K8 Go to UniProtKB: Q8A6K8 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8A6K8 | ||||
Protein Feature ViewExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TRS Query on TRS | J [auth A] | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O |  | Ligand Interaction | |
| GOL Query on GOL | F [auth A], G [auth A], H [auth A], I [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | D [auth A], E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
| MG Query on MG | B [auth A], C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.53 Å
- R-Value Free: 0.164
- R-Value Work: 0.149
- R-Value Observed: 0.150
- Space Group: P 43
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 83.804 | α = 90 |
| b = 83.804 | β = 90 |
| c = 43.366 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| MLPHARE | phasing |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2015-06-12
- Released Date: 2015-07-01 Deposition Author(s): Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM094585 |
Revision History (Full details and data files)
- Version 1.0: 2015-07-01
Type: Initial release - Version 1.1: 2017-09-27
Changes: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary - Version 1.2: 2019-12-25
Changes: Author supporting evidence
