8SD5

Crystal structure of HPPK from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb8SD5/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-06 Released: 2024-07-03 
• Deposition Author(s): Shaw, G.X., Needle, D., Stair, N.R., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 

Starting Model: experimental

Literature

Crystal structure of HPPK from Methanocaldococcus jannaschii

Shaw, G.X., Needle, D., Stair, N.R., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.77 kDa 
• Atom Count: 7,003 
• Modelled Residue Count: 858 
• Deposited Residue Count: 964 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase	A, B, C, D	241	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: mptE, MJ1634 EC: 2.7.6.3
UniProt
Find proteins for Q59028 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q59028  Go to UniProtKB:  Q59028

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth B], G [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.290 
• R-Value Work: 0.243 
• R-Value Observed: 0.245 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.729	α = 90
b = 75.744	β = 90
c = 179.578	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-03 
Deposition Author(s): Shaw, G.X., Needle, D., Stair, N.R., Cherry, S., Tropea, J.E., Waugh, D.S., Ji, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2024-07-03
  Type: Initial release