Download MendeleyCrystal structure of YdeN-like protein of unknown function (DUF1234) (YP_051181.1) from Erwinia carotovora subsp. atroseptica SCRI1043 at 1.66 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
3BDV
Crystal structure of a putative yden-like hydrolase (eca3091) from pectobacterium atrosepticum scri1043 at 1.66 A resolution
- PDB DOI: https://doi.org/10.2210/pdb3BDV/pdb
- Classification: HYDROLASE
- Organism(s): Pectobacterium atrosepticum SCRI1043
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2007-11-15 Released: 2007-11-27
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.213
- R-Value Work: 0.170
- R-Value Observed: 0.173
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 |
| Uncharacterized protein DUF1234 | 191 | Pectobacterium atrosepticum SCRI1043 | Mutation(s): 0 Gene Names: YP_051181.1, ECA3091 |  | |
UniProt | |||||
Find proteins for Q6D2K4 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6D2K4 Go to UniProtKB: Q6D2K4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6D2K4 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EDO Query on EDO | F [auth A], G [auth A], H [auth A], K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| CA Query on CA | C [auth A], D [auth A], I [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | E [auth A], J [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.66 Å
- R-Value Free: 0.213
- R-Value Work: 0.170
- R-Value Observed: 0.173
- Space Group: P 21 21 21
- Diffraction Data: https://doi.org/10.18430/M33BDV
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 35.655 | α = 90 |
| b = 93.302 | β = 90 |
| c = 104.095 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHENIX | refinement |
| SHELX | phasing |
| MolProbity | model building |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
| XDS | data reduction |
| autoSHARP | phasing |
Entry History
Deposition Data
- Released Date: 2007-11-27 Deposition Author(s): Joint Center for Structural Genomics (JCSG)
Revision History (Full details and data files)
- Version 1.0: 2007-11-27
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2017-10-25
Changes: Refinement description - Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description - Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
