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Download EndnoteCrystal structure of a PDZ domain protein (BDI_1242) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
4L8N
Crystal structure of a PDZ domain protein (BDI_1242) from Parabacteroides distasonis ATCC 8503 at 2.50 A resolution
- DOI: 10.2210/pdb4L8N/pdb
- Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION
- Organism(s): Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)
- Expression System: Escherichia coli
- Deposited: 2013-06-17 Released: 2013-06-26
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.5 Å
- R-Value Free: 0.220
- R-Value Work: 0.186
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| PDZ domain protein | A | 457 | Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152) | Mutation(s): 0 |
Find proteins for A6LBD9 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Go to UniProtKB: A6LBD9 | ||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MG Query on MG | A | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | Ligand Interaction | |
| MPD Query on MPD | A | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | Ligand Interaction | |
| EOH Query on EOH | A | ETHANOL C2 H6 O LFQSCWFLJHTTHZ-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: 2.5 Å
- R-Value Free: 0.220
- R-Value Work: 0.186
- Space Group: P 31 2 1
- Diffraction Data DOI:
10.18430/M34L8N Protein Diffraction
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 104.093 | α = 90.00 |
| b = 104.093 | β = 90.00 |
| c = 96.277 | γ = 120.00 |
| Software Name | Purpose |
|---|---|
| BUSTER-TNT | refinement |
| BUSTER | refinement |
| XSCALE | data scaling |
| XDS | data reduction |
| SHELX | phasing |
| MolProbity | model building |
| PDB_EXTRACT | data extraction |
| SHARP | phasing |
| SHELXD | phasing |
Entry History
Deposition Data
- Deposited Date: 2013-06-17
- Released Date: 2013-06-26
- Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History
- Version 1.0: 2013-06-26
Type: Initial release - Version 1.1: 2017-11-15
Type: Refinement description
