3C11 | pdb_00003c11

Yeast Hsp82 N-terminal domain-Geldanamycin complex: effects of mutants 98-99 KS-AA

• PDB DOI: https://doi.org/10.2210/pdb3C11/pdb

• Classification: CHAPERONE/Antibiotic
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-01-21 Released: 2008-07-29 
• Deposition Author(s): Immormino, R.M., Gewirth, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.188 (DCC) 

Starting Model: experimental

Literature

Crystal Structure of GRP94 with the Specific Mutation KS168-169AA with Bound Geldanamycin

Immormino, R.M., Metzger IV, L.E., Reardon, P.N., Gewirth, D.T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.72 kDa 
• Atom Count: 2,175 
• Modeled Residue Count: 214 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent molecular chaperone HSP82	A	240	Saccharomyces cerevisiae	Mutation(s): 2  Gene Names: HSP82, HSP90
UniProt
Find proteins for P02829 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02829  Go to UniProtKB:  P02829

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDM	B [auth A]	GELDANAMYCIN C29 H40 N2 O9 QTQAWLPCGQOSGP-KSRBKZBZSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.188 (DCC) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.15	α = 90
b = 74.15	β = 90
c = 110.88	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Immormino, R.M., Gewirth, D.T.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2012-02-29
  Changes: Non-polymer description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description