3MII | pdb_00003mii

Crystal structure of Y0R391Cp/HSP33 from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3MII/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-10 Released: 2010-12-08 
• Deposition Author(s): Guo, P.-C., Zhou, Y.-Y., Zhou, C.-Z., Li, W.-F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structure of Hsp33/YOR391Cp from the yeast Saccharomyces cerevisiae

Guo, P.-C., Zhou, Y.-Y., Ma, X.-X., Li, W.-F.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1557-1561

• PubMed: 21139195 
• DOI: https://doi.org/10.1107/S1744309110039965
• Primary Citation Related Structures: 
  3MII


• PubMed Abstract: 
  

  Saccharomyces cerevisiae Hsp33/YOR391Cp is a member of the ThiI/DJ-1/PfpI superfamily. Hsp33 was overexpressed in Escherichia coli and its crystal structure was determined at 2.40 Å resolution. Structural comparison revealed that Hsp33 adopts an α/β-hydrolase fold and possesses the putative Cys-His-Glu catalytic triad common to the Hsp31 family, suggesting that Hsp33 and Hsp31 share similar aminopeptidase activity, while structural deviations in helices α2-α3 of the core domain might be responsible for the access of different peptide substrates.

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Organizational Affiliation: 
• Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.47 kDa 
• Atom Count: 3,834 
• Modeled Residue Count: 469 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable chaperone protein HSP33	A, B	245	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YOR091C EC: 3.2 (PDB Primary Data), 4.2.1.130 (UniProt)
UniProt
Find proteins for Q08914 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08914  Go to UniProtKB:  Q08914

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A], F [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.42	α = 90
b = 96.42	β = 90
c = 132.23	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-08 
Deposition Author(s): Guo, P.-C., Zhou, Y.-Y., Zhou, C.-Z., Li, W.-F.

Revision History  

• Version 1.0: 2010-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-22
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary