Download MendeleyCrystal Structure of Calcineurin-like Phosphoesterase from Bacillus subtilis
Kim, Y., Marshall, N., Cobb, G., Joachimiak, A.To be published.
3GVE
Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis
- PDB DOI: https://doi.org/10.2210/pdb3GVE/pdb
- Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
- Organism(s): Bacillus subtilis subsp. subtilis str. 168
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-03-30 Released: 2009-04-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.163
- R-Value Work: 0.154
- R-Value Observed: 0.154
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 |
| YfkN protein | 341 | Bacillus subtilis subsp. subtilis str. 168 | Mutation(s): 0 Gene Names: BSU07840, yfkN EC: 3.1.3.6 (UniProt), 3.1.3.5 (UniProt), 3.1.4.16 (UniProt) |  | |
UniProt | |||||
Find proteins for O34313 (Bacillus subtilis (strain 168)) Explore O34313 Go to UniProtKB: O34313 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O34313 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | E [auth A], I [auth B] | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | ||
| MN Query on MN | C [auth A], F [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| MG Query on MG | D [auth A], G [auth B], H [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
| 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: 1.25 Å
- R-Value Free: 0.163
- R-Value Work: 0.154
- R-Value Observed: 0.154
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 67.091 | α = 90 |
| b = 92.505 | β = 89.94 |
| c = 50.316 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| SHELXCD | phasing |
| SHELXD | phasing |
| MLPHARE | phasing |
| DM | model building |
| SOLVE | phasing |
| RESOLVE | model building |
| PHENIX | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| DM | phasing |
| RESOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2009-04-28 Deposition Author(s): Kim, Y., Marshall, N., Cobb, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-04-28
Type: Initial release - Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance - Version 1.2: 2017-11-01
Changes: Refinement description - Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary
