8SBU | pdb_00008sbu

Crystal structure of MBP fusion with HPPK from Methanocaldococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb8SBU/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12, Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2023-04-04 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: 2.20 Å
• R-Value Free: 
  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MBP fusion with 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)

Macromolecule Content 

• Total Structure Weight: 138.13 kDa 
• Atom Count: 9,492 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin-binding periplasmic protein,6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase	A, B	618	Escherichia coli K-12, Methanocaldococcus jannaschii DSM 2661 This entity is chimeric	Mutation(s): 12  Gene Names: malE, b4034, JW3994, mptE, MJ1634 EC: 2.7.6.3
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q59028 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q59028  Go to UniProtKB:  Q59028
UniProt Groups	P0AEX9Q59028

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.17	α = 67.44
b = 69.827	β = 74.63
c = 73.121	γ = 78.13

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