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 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.176 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.149 (Depositor) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.75 kDa 
• Atom Count: 1,692 
• Modeled Residue Count: 176 
• Deposited Residue Count: 183 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative phosphoribosyltransferase	A	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, WHON_02375C, WHOU_01208, WHOU_02454C, WHOV_00719, WHOV_02442C, WHOW_01101, WHOW_02437C, WHOX_00398, WHOX_02372C, WHOZ_01227, WHOZ_02445C
UniProt
Find proteins for A0A1D3HIA2 (Neisseria gonorrhoeae) Explore A0A1D3HIA2  Go to UniProtKB:  A0A1D3HIA2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	D [auth A]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N
EDO	B [auth A], C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
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), 0.212 (DCC) 
• R-Value Work:  0.149 (Depositor) 
• 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 Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-24 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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