7YCJ | pdb_00007ycj

Crystal structure of Vac8 bound to Vac17

• PDB DOI: https://doi.org/10.2210/pdb7YCJ/pdb

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-01 Released: 2023-07-12 
• Deposition Author(s): Kim, H., Kim, H., Lee, C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Vac8 bound to Vac17

Kim, H., Park, J., Kim, H., Ko, N., Park, J., Lee, C., Jun, Y.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.33 kDa 
• Atom Count: 4,282 
• Modeled Residue Count: 536 
• Deposited Residue Count: 563 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein 8	A	507	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: VAC8, YEB3, YEL013W
UniProt
Find proteins for P39968 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39968  Go to UniProtKB:  P39968

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
vacuole-related protein 17	B	56	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: VAC17, YCL063W, YCL63W/YCL62W
UniProt
Find proteins for P25591 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25591  Go to UniProtKB:  P25591

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.446	α = 90
b = 147.446	β = 90
c = 121.514	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-12 
Deposition Author(s): Kim, H., Kim, H., Lee, C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021M3A9G8022417
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2022R1A2C1007314
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C2009550

Revision History  

• Version 1.0: 2023-07-12
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description