Download MendeleyThe structure of a DegV family protein from Eubacterium eligens.
Cuff, M.E., Hendricks, R., Freeman, L., Joachimiak, A.To be published.
3FDJ
The structure of a DegV family protein from Eubacterium eligens.
- PDB DOI: https://doi.org/10.2210/pdb3FDJ/pdb
- Classification: structural genomics, unknown function
- Organism(s): Lachnospira eligens
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2008-11-25 Released: 2009-02-03
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.191
- R-Value Work: 0.160
- R-Value Observed: 0.162
wwPDB Validation 3D Report Full Report
This is version 1.4 of the entry. See complete history.
Re-refinement Note
A newer entry is available that reflects an alternative modeling of the original data: 5UXY
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| DegV family protein | 278 | Lachnospira eligens | Mutation(s): 0 Gene Names: ASSEMBLY.20070618:0-0:0-0 (zvnW5vjFOAACMF8NLOPRFTmWH60:01:1-275) |  | |
UniProt | |||||
Find proteins for D0VX07 (Lachnospira eligens) Explore D0VX07 Go to UniProtKB: D0VX07 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | D0VX07 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| P6G Query on P6G | B [auth A] | HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N |  | ||
| PG4 Query on PG4 | D [auth A] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | C [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| ACY Query on ACY | F [auth A] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |  | ||
| NA Query on NA | E [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| 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: 1.80 Å
- R-Value Free: 0.191
- R-Value Work: 0.160
- R-Value Observed: 0.162
- Space Group: P 41 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 57.445 | α = 90 |
| b = 57.445 | β = 90 |
| c = 186.558 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| MLPHARE | phasing |
| DM | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| SBC-Collect | data collection |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| HKL-3000 | phasing |
| SHELXD | phasing |
| SHELXE | model building |
| SOLVE | phasing |
| RESOLVE | phasing |
| ARP/wARP | model building |
| CCP4 | phasing |
| O | model building |
| Coot | model building |
Entry History
Deposition Data
- Released Date: 2009-02-03 Deposition Author(s): Cuff, M.E., Hendricks, R., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-02-03
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2023-12-27
Changes: Data collection, Database references, Derived calculations - Version 1.4: 2024-10-16
Changes: Structure summary
