5KBX | pdb_00005kbx

Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

• PDB DOI: https://doi.org/10.2210/pdb5KBX/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli DH5[alpha], Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-06-03 Released: 2017-06-07 
• Deposition Author(s): Menon, S.K., West, A.H.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.233 (Depositor) 

Literature

Insights revealed by the co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

Menon, S.K., Branscum, K.M., Foster, C.A., West, A.H.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 44.11 kDa 
• Atom Count: 2,435 
• Modeled Residue Count: 297 
• Deposited Residue Count: 385 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphorelay intermediate protein YPD1	A	167	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YPD1, YDL235C, D0790
UniProt
Find proteins for Q07688 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07688  Go to UniProtKB:  Q07688

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Osmolarity two-component system protein SSK1	B	218	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: SSK1, YLR006C
UniProt
Find proteins for Q07084 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q07084  Go to UniProtKB:  Q07084

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	C [auth A], E [auth B], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.279 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.233 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.696	α = 90
b = 71.696	β = 90
c = 176.389	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-06-07 
Deposition Author(s): Menon, S.K., West, A.H.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB 1158319

Revision History  

• Version 1.0: 2017-06-07
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 2.0: 2019-10-23
  Type: Coordinate replacement
  Reason: Atomic clashes
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2019-11-27
  Changes: Author supporting evidence
• Version 2.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary