3HT2 | pdb_00003ht2

Zink containing polyketide cyclase RemF from Streptomyces resistomycificus

• PDB DOI: https://doi.org/10.2210/pdb3HT2/pdb

• Classification: LYASE
• Organism(s): Streptomyces resistomycificus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-11 Released: 2009-10-13 
• Deposition Author(s): Silvennoinen, L., Sandalova, T., Schneider, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.244 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

The polyketide cyclase RemF from Streptomyces resistomycificus contains an unusual octahedral zinc binding site

Silvennoinen, L., Sandalova, T., Schneider, G.

(2009) FEBS Lett 583: 2917-2921

• PubMed: 19665022 
• DOI: https://doi.org/10.1016/j.febslet.2009.07.061
• Primary Citation Related Structures: 
  3HT1, 3HT2


• PubMed Abstract: 
  

  RemF is a polyketide cyclase involved in the biosynthesis of the aromatic pentacyclic metabolite resistomycin in Streptomyces resistomycificus. The enzyme is a member of a structurally hitherto uncharacterized class of polyketide cyclases. The crystal structure of RemF was determined by SAD and refined to 1.2 A resolution. The enzyme subunit shows a beta-sandwich structure with a topology characteristic for the cupin fold. RemF contains a metal binding site located at the bottom of the predominantly hydrophobic active site cavity. A zinc ion is coordinated to four histidine side chains, and two water molecules in octahedral ligand sphere geometry, highly unusual for zinc binding sites in proteins.

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Organizational Affiliation: 
• Department of Medical Biophysics and Biochemistry, Karolinska Institutet, Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.27 kDa 
• Atom Count: 2,531 
• Modeled Residue Count: 286 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RemF protein	A, B [auth C]	145	Streptomyces resistomycificus	Mutation(s): 0  Gene Names: remF
UniProt
Find proteins for Q70DX5 (Streptomyces resistomycificus) Explore Q70DX5  Go to UniProtKB:  Q70DX5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B [auth C]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.244 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.433	α = 90
b = 97.255	β = 91.99
c = 47.743	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
SOLVE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Silvennoinen, L., Sandalova, T., Schneider, G.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary