8OOM

Structural and functional studies of geldanamycin amide synthase ShGdmF

• PDB DOI: https://doi.org/10.2210/pdb8OOM/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Streptomyces hygroscopicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-04-05 Released: 2024-04-17 
• Deposition Author(s): Ewert, W., Zeilinger, C., Kirschning, A., Preller, M.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Starting Model: experimental

Literature

Structural and functional studies of geldanamycin amide synthase ShGdmF

Ewert, W., Bartens, C., Heutling, A., Ongouta, J., Vogt, M., Kishore, A., Zeilinger, C., Preller, M.

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: 30.31 kDa 
• Atom Count: 2,121 
• Modelled Residue Count: 246 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GdmF	A	263	Streptomyces hygroscopicus	Mutation(s): 0  Gene Names: gdmF
UniProt
Find proteins for Q84G21 (Streptomyces hygroscopicus) Explore Q84G21  Go to UniProtKB:  Q84G21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PNY (Subject of Investigation/LOI)	B [auth A]	(2R)-2,4-dihydroxy-3,3-dimethyl-N-{3-oxo-3-[(2-sulfanylethyl)amino]propyl}butanamide C11 H22 N2 O4 S ZNXZGRMVNNHPCA-VIFPVBQESA-N
ACT	C [auth A], D [auth A], E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.82 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.874	α = 90
b = 96.184	β = 90
c = 86.754	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHENIX	refinement
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-17 
Deposition Author(s): Ewert, W., Zeilinger, C., Kirschning, A., Preller, M.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-04-17
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Structure summary