Download MendeleyDFT Studies of the Rate-Limiting Step in the Reaction Cycle of the Fe/2OG Dioxygenase AlkB and Related Experimental Studies
Hall, M.L., Ergel, B., Miller, E.B., Yu, B., Rinaldo, D., Hunt, J.F., Friesner, R.To be published.
4ZHN
Crystal Structure of AlkB T208A mutant protein in complex with Co(II), 2-oxoglutarate, and methylated trinucleotide T-meA-T
- PDB DOI: https://doi.org/10.2210/pdb4ZHN/pdb
- NAKB: 4ZHN
- Classification: Oxidoreductase/DNA
- Organism(s): synthetic construct, Escherichia coli K-12
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2015-04-25 Released: 2015-12-23
- Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.147
- R-Value Work: 0.118
- R-Value Observed: 0.119
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: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Alpha-ketoglutarate-dependent dioxygenase AlkB | B [auth A] | 211 | Escherichia coli K-12 | Mutation(s): 1 Gene Names: alkB, aidD, b2212, JW2200 EC: 1.14.11.33 |  |
UniProt | |||||
Find proteins for P05050 (Escherichia coli (strain K12)) Explore P05050 Go to UniProtKB: P05050 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P05050 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| methylated trinucleotide DNA T-meA-T | A [auth B] | 3 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| AKG Query on AKG | D [auth A] | 2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N |  | ||
| CO Query on CO | C [auth A] | COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.33 Å
- R-Value Free: 0.147
- R-Value Work: 0.118
- R-Value Observed: 0.119
- Space Group: P 43
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 41.373 | α = 90 |
| b = 41.373 | β = 90 |
| c = 116.569 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| Coot | model building |
| HKL-2000 | data scaling |
| HKL-2000 | data reduction |
| COMO | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-12-23 Deposition Author(s): Ergel, B., Yu, B., Vorobiev, S.M., Forouhar, F., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | 1R01GM077360 |
Revision History (Full details and data files)
- Version 1.0: 2015-12-23
Type: Initial release - Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations - Version 1.2: 2017-11-29
Changes: Database references - Version 1.3: 2019-12-25
Changes: Author supporting evidence - Version 1.4: 2023-09-27
Changes: Data collection, Database references, Refinement description
