4KYD

Partial Structure of the C-terminal domain of the HPIV4B phosphoprotein, fused to MBP.

• PDB DOI: https://doi.org/10.2210/pdb4KYD/pdb

• Classification: binding protein, viral protein
• Organism(s): Escherichia coli K-12, Human parainfluenza virus 4b (strain 68-333)
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2013-05-28 Released: 2013-09-25 
• Deposition Author(s): Yegambaram, K., Bulloch, E.M.M., Kingston, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.222 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 93.85 kDa 
• Atom Count: 6,517 
• Modelled Residue Count: 801 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein, Phosphoprotein, chimeric construct	A, B	420	Escherichia coli K-12, Human parainfluenza virus 4b (strain 68-333) This entity is chimeric	Mutation(s): 6  Gene Names: b4034, JW3994, malE, P, P/V
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for P21738 (Human parainfluenza 4b virus (strain 68-333)) Explore P21738  Go to UniProtKB:  P21738
UniProt Groups	P21738P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N

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: 2.21 Å
• R-Value Free: 0.222 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.83	α = 90
b = 142.83	β = 90
c = 114.312	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Yegambaram, K., Bulloch, E.M.M., Kingston, R.L.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 1.1: 2013-11-13
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2018-01-24
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary