Download MendeleyCrystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
Dranow, D.M., Abendroth, J., Lorimer, D.D., Edwards, T.E.To be published.
5VOG | pdb_00005vog
Crystal Structure of a Hypothetical Protein from Neisseria gonorrhoeae with bound ppGpp
- PDB DOI: https://doi.org/10.2210/pdb5VOG/pdb
- Classification: TRANSFERASE
- Organism(s): Neisseria gonorrhoeae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2017-05-02 Released: 2017-05-24
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.176 (Depositor), 0.180 (DCC)
- R-Value Work: 0.149 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.151 (Depositor)
Starting Model: experimental
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This is version 1.3 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 |
| Putative phosphoribosyltransferase | 183 | Neisseria gonorrhoeae | Mutation(s): 0 Gene Names: ESCNG_40048, WHOF_00431, WHOF_02526C, WHOG_01129, WHOG_02374C, WHOK_01250, WHOK_02372C, WHOM_00300, WHOM_02380C, WHON_00453... |  | |
UniProt | |||||
Find proteins for A0A1D3HIA2 (Neisseria gonorrhoeae) Explore A0A1D3HIA2 Go to UniProtKB: A0A1D3HIA2 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A1D3HIA2 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| G4P Query on G4P | D [auth A] | GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N |  | ||
| EDO Query on EDO | B [auth A], C [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| MG Query on MG | E [auth A], F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.50 Å
- R-Value Free: 0.176 (Depositor), 0.180 (DCC)
- R-Value Work: 0.149 (Depositor), 0.150 (DCC)
- R-Value Observed: 0.151 (Depositor)
Diffraction Data: https://doi.org/10.18430/M35VOG
Space Group: F 2 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 81.27 | α = 90 |
| b = 103.93 | β = 90 |
| c = 105.54 | γ = 90 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MoRDa | phasing |
Entry History
Deposition Data
- Released Date: 2017-05-24 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2017-05-24
Type: Initial release - Version 1.1: 2017-05-31
Changes: Data collection - Version 1.2: 2017-07-05
Changes: Database references - Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
