Download MendeleyCrystal Structure of a Histone Deacetylase superfamily protein from Burkholderia phymatumphymatum
Dranow, D.M., Abendroth, J., Lorimer, D., Edwards, T.E.To be published.
5JI5
Crystal Structure of a Histone Deacetylase superfamily protein from Burkholderia phymatumphymatum
- PDB DOI: https://doi.org/10.2210/pdb5JI5/pdb
- Classification: HYDROLASE
- Organism(s): Paraburkholderia phymatum STM815
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2016-04-21 Released: 2016-05-04
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235
- R-Value Work: 0.169
- R-Value Observed: 0.175
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| BuphA.10154.a.B1 | 315 | Paraburkholderia phymatum STM815 | Mutation(s): 0 Gene Names: Bphy_0756 |  | |
UniProt | |||||
Find proteins for B2JF16 (Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815)) Explore B2JF16 Go to UniProtKB: B2JF16 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B2JF16 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| SO4 Query on SO4 | C [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| ZN Query on ZN | B [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | D [auth A], E [auth A], F [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| NA Query on NA | G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.235
- R-Value Work: 0.169
- R-Value Observed: 0.175
- Space Group: C 2 2 21
- Diffraction Data: https://doi.org/10.18430/M35JI5
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.38 | α = 90 |
| b = 127.87 | β = 90 |
| c = 68.68 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| XSCALE | data scaling |
| MR-Rosetta | phasing |
Entry History
Deposition Data
- Released Date: 2016-05-04 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2016-05-04
Type: Initial release - Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
