4XS7

Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb4XS7/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces peucetius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-22 Released: 2016-01-27 
• Deposition Author(s): Jackson, D.R., Valentic, T.R., Tsai, S.C., Patel, A., Mohammed, L., Vasilakis, K., Wattana-amorn, P., Long, P.F., Crump, M.P., Crosby, J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Determining the Molecular Basis for Starter Unit Selection During Daunorubicin Biosynthesis

Jackson, D.R., Valentic, T.R., Tsai, S.C., Patel, A., Mohammed, L., Vasilakis, K., Wattana-amorn, P., Long, P.F., Crump, M.P., Crosby, J.

To be published.

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: 78.95 kDa 
• Atom Count: 5,316 
• Modelled Residue Count: 680 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Daunorubicin-doxorubicin polyketide synthase	A, B	373	Streptomyces peucetius	Mutation(s): 0  Gene Names: dpsC EC: 2.3.1
UniProt
Find proteins for Q54816 (Streptomyces peucetius) Explore Q54816  Go to UniProtKB:  Q54816

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OAS	A, B	L-PEPTIDE LINKING	C5 H9 N O4		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.213	α = 90
b = 91.213	β = 90
c = 315.643	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Jackson, D.R., Valentic, T.R., Tsai, S.C., Patel, A., Mohammed, L., Vasilakis, K., Wattana-amorn, P., Long, P.F., Crump, M.P., Crosby, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM100305-03

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary