Download MendeleyCrystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and its Catalytic Mechanism
Li, D., Caffrey, M.To be published.
4CJZ
Crystal structure of the integral membrane diacylglycerol kinase DgkA- 9.9, delta 4
- PDB DOI: https://doi.org/10.2210/pdb4CJZ/pdb
- Classification: TRANSFERASE
- Organism(s): Escherichia coli K-12
- Expression System: Escherichia coli
- Mutation(s): Yes
- Membrane Protein: Yes PDBTMMemProtMD
- Deposited: 2013-12-23 Released: 2015-01-28
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.291
- R-Value Work: 0.255
- R-Value Observed: 0.257
Starting Model: experimental
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This is version 1.5 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 |
| DIACYLGLYCEROL KINASE | 130 | Escherichia coli K-12 | Mutation(s): 4 EC: 2.7.1.107 Membrane Entity: Yes |  | |
UniProt | |||||
Find proteins for P0ABN1 (Escherichia coli (strain K12)) Explore P0ABN1 Go to UniProtKB: P0ABN1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0ABN1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OLC Query on OLC | D [auth C] | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 3.25 Å
- R-Value Free: 0.291
- R-Value Work: 0.255
- R-Value Observed: 0.257
- Space Group: P 31 2 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 72.78 | α = 90 |
| b = 72.78 | β = 90 |
| c = 199.28 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
Entry History
Deposition Data
- Released Date: 2015-01-28 Deposition Author(s): Li, D., Aragao, D., Pye, V.E., Caffrey, M.
Revision History (Full details and data files)
- Version 1.0: 2015-01-28
Type: Initial release - Version 1.1: 2016-11-16
Changes: Database references - Version 1.2: 2019-03-06
Changes: Data collection, Experimental preparation, Other - Version 1.3: 2019-04-03
Changes: Data collection, Experimental preparation - Version 1.4: 2023-03-29
Changes: Database references, Derived calculations, Other, Structure summary - Version 1.5: 2024-02-07
Changes: Data collection, Refinement description
