Download MendeleyCrystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
4QHZ
Crystal structure of a putative glycosyl hydrolase (BDI_3914) from Parabacteroides distasonis ATCC 8503 at 2.13 A resolution
- PDB DOI: https://doi.org/10.2210/pdb4QHZ/pdb
- Classification: HYDROLASE
- Organism(s): Parabacteroides distasonis ATCC 8503
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2014-05-30 Released: 2014-07-30
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.203
- R-Value Work: 0.171
- R-Value Observed: 0.172
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 |
| putative glycosyl hydrolase | 246 | Parabacteroides distasonis ATCC 8503 | Mutation(s): 0 Gene Names: BDI_3914 |  | |
UniProt | |||||
Find proteins for A6LIT1 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LIT1 Go to UniProtKB: A6LIT1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A6LIT1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | E [auth A], H [auth C], J [auth D] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | F [auth A], G [auth B], I [auth C], K [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| Modified Residues 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MLY Query on MLY | A, B, C, D | L-PEPTIDE LINKING | C8 H18 N2 O2 |  | LYS |
| MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.13 Å
- R-Value Free: 0.203
- R-Value Work: 0.171
- R-Value Observed: 0.172
- Space Group: P 1 21 1
- Diffraction Data: https://doi.org/10.18430/M34QHZ
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.774 | α = 90 |
| b = 144.763 | β = 101.27 |
| c = 82.452 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SOLVE | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
Entry History
Deposition Data
- Released Date: 2014-07-30 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2014-07-30
Type: Initial release - Version 1.1: 2017-11-22
Changes: Refinement description - Version 1.2: 2018-01-24
Changes: Database references - Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
