Download MendeleyCrystal Structure of Activated Pled, Identification of Dimerization and Catalysis Relevant Regulatory Mechanisms
Wassmann, P., Massa, C., Zaehringer, F., Schirmer, T.To be published.
2WB4
activated diguanylate cyclase PleD in complex with c-di-GMP
- PDB DOI: https://doi.org/10.2210/pdb2WB4/pdb
- Classification: TRANSFERASE
- Organism(s): Caulobacter vibrioides CB15
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2009-02-20 Released: 2010-04-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.268
- R-Value Work: 0.239
- R-Value Observed: 0.241
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 |
| DIGUANYLATE CYCLASE | 459 | Caulobacter vibrioides CB15 | Mutation(s): 0 EC: 2.7.7.65 (PDB Primary Data), 4.6.1 (PDB Primary Data) |  | |
UniProt | |||||
Find proteins for B8GZM2 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore B8GZM2 Go to UniProtKB: B8GZM2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B8GZM2 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| C2E Query on C2E | E [auth A], F [auth A], K [auth B], L [auth B], M [auth B] | 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N |  | ||
| SO4 Query on SO4 | G [auth A], H [auth A], O [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| BEF Query on BEF | C [auth A], I [auth B] | BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K |  | ||
| MG Query on MG | D [auth A], J [auth B], N [auth B] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.268
- R-Value Work: 0.239
- R-Value Observed: 0.241
- Space Group: P 21 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 123.56 | α = 90 |
| b = 127.43 | β = 90 |
| c = 88.13 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2010-04-21 Deposition Author(s): Wassmann, P., Schirmer, T.
Revision History (Full details and data files)
- Version 1.0: 2010-04-21
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary
