Download MendeleyCrystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes
Klimecka, M.M., Chruszcz, M., Zimmerman, M.D., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W.To be published.
3KZP
Crystal structure of putative diguanylate cyclase/phosphodiesterase from Listaria monocytigenes
- PDB DOI: https://doi.org/10.2210/pdb3KZP/pdb
- Classification: Structural Genomics, Unknown function
- Organism(s): Listeria monocytogenes
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-12-08 Released: 2009-12-22
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.239
- R-Value Work: 0.185
- R-Value Observed: 0.187
wwPDB Validation 3D Report Full Report
This is version 1.2 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 diguanylate cyclase/phosphodiesterase | 235 | Listeria monocytogenes | Mutation(s): 0 Gene Names: lmo0111 |  | |
UniProt | |||||
Find proteins for Q8YAK7 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8YAK7 Go to UniProtKB: Q8YAK7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8YAK7 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CAC Query on CAC | H [auth A], L [auth B] | CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M |  | ||
| CA Query on CA | G [auth A], J [auth B] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A] D [auth A] E [auth A] F [auth A] I [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: 2.00 Å
- R-Value Free: 0.239
- R-Value Work: 0.185
- R-Value Observed: 0.187
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 59.766 | α = 90 |
| b = 92.04 | β = 90 |
| c = 96.21 | γ = 90 |
| Software Name | Purpose |
|---|---|
| HKL-3000 | data collection |
| HKL-3000 | phasing |
| MLPHARE | phasing |
| DM | model building |
| SHELXD | phasing |
| RESOLVE | model building |
| ARP/wARP | model building |
| REFMAC | refinement |
| Coot | model building |
| HKL-3000 | data reduction |
| HKL-2000 | data scaling |
| DM | phasing |
| RESOLVE | phasing |
Entry History
Deposition Data
- Released Date: 2009-12-22 Deposition Author(s): Klimecka, M.M., Chruszcz, M., Zimmerman, M.D., Kudritska, M., Savchenko, A., Edwards, A., Joachimiak, A., Minor, W., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-12-22
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2022-04-13
Changes: Database references, Derived calculations, Structure summary
