3H0X | pdb_00003h0x

Crystal structure of peptide-binding domain of Kar2 protein from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3H0X/pdb

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


• Deposited: 2009-04-10 Released: 2009-04-21 
• Deposition Author(s): Osipiuk, J., Bigelow, L., Gu, M., Sahi, C., Craig, E.A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

X-ray crystal structure of peptide-binding domain of Kar2 protein from Saccharomyces cerevisiae.

Osipiuk, J., Bigelow, L., Gu, M., Sahi, C., Craig, E.A., Joachimiak, A.

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.41 kDa 
• Atom Count: 1,308 
• Modeled Residue Count: 150 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
78 kDa glucose-regulated protein homolog	A	152	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: GRP78, J1248, KAR2, SSD1, YJL034W EC: 3.6.4.10
UniProt
Find proteins for P16474 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16474  Go to UniProtKB:  P16474

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.846	α = 90
b = 103.113	β = 90
c = 80.792	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	phasing
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Osipiuk, J., Bigelow, L., Gu, M., Sahi, C., Craig, E.A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description