Download MendeleyThe Structure of the DNA-binding Domain of the Class III ETS-Family Member SpiD from Raja eglanteria
Terrell, J.R., Vernon, T.N., Poon, G.M.K.To be published.
9D2X
SpiD ETS-domain (168-273) in complex with the DNA sequence d(AATAAAAGGAAGTGGG)
- PDB DOI: https://doi.org/10.2210/pdb9D2X/pdb
- NAKB: 9D2X
- Classification: TRANSCRIPTION/DNA
- Organism(s): synthetic construct, Rostroraja eglanteria
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2024-08-09 Released: 2024-10-30
- Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.270
- R-Value Work: 0.221
- R-Value Observed: 0.226
Starting Model: experimental
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wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| SpiD | C [auth F], F [auth E] | 107 | Rostroraja eglanteria | Mutation(s): 0 |  |
UniProt | |||||
Find proteins for Q9DEW5 (Raja eglanteria) Explore Q9DEW5 Go to UniProtKB: Q9DEW5 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9DEW5 | ||||
Sequence AnnotationsExpand | |||||
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Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3') | A [auth C], D [auth A] | 16 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
| |||||
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3') | B [auth D], E [auth B] | 16 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| EPE Query on EPE | G [auth B] | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.29 Å
- R-Value Free: 0.270
- R-Value Work: 0.221
- R-Value Observed: 0.226
- Space Group: P 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 36.934 | α = 79.209 |
| b = 42.939 | β = 81.529 |
| c = 62.534 | γ = 76.185 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-10-30 Deposition Author(s): Terrell, J.R., Vernon, T.N., Poon, G.M.K.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) | United States | HL155178 |
| National Science Foundation (NSF, United States) | United States | MCB2028902 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | GM137160 |
Revision History (Full details and data files)
- Version 1.0: 2024-10-30
Type: Initial release
