6APK | pdb_00006apk

Trans-acting transferase from Disorazole synthase solved by serial femtosecond XFEL crystallography

• PDB DOI: https://doi.org/10.2210/pdb6APK/pdb

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


• Deposited: 2017-08-17 Released: 2018-04-04 
• Deposition Author(s): Lyubimov, A.Y., Mathews, I.I., Uervivojnangkoorn, M., Khosla, C., Soltis, S.M., Cohen, A.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography.

Mathews, I.I., Allison, K., Robbins, T., Lyubimov, A.Y., Uervirojnangkoorn, M., Brunger, A.T., Khosla, C., DeMirci, H., McPhillips, S.E., Hollenbeck, M., Soltis, M., Cohen, A.E.

(2017) Biochemistry 56: 4751-4756

• PubMed: 28832129 
• DOI: https://doi.org/10.1021/acs.biochem.7b00711
• Primary Citation Related Structures: 
  6APF, 6APG, 6APK, 6APM


• PubMed Abstract: 
  

  The crystal structure of the trans-acyltransferase (AT) from the disorazole polyketide synthase (PKS) was determined at room temperature to a resolution of 2.5 Å using a new method for the direct delivery of the sample into an X-ray free-electron laser. A novel sample extractor efficiently delivered limited quantities of microcrystals directly from the native crystallization solution into the X-ray beam at room temperature. The AT structure revealed important catalytic features of this core PKS enzyme, including the occurrence of conformational changes around the active site. The implications of these conformational changes for polyketide synthase reaction dynamics are discussed.

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Organizational Affiliation: 
• Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.66 kDa 
• Atom Count: 2,238 
• Modeled Residue Count: 282 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DisD protein	A	282	Sorangium cellulosum	Mutation(s): 0  Gene Names: dszD, disD EC: 2.3.1.39
UniProt
Find proteins for Q4U443 (Sorangium cellulosum) Explore Q4U443  Go to UniProtKB:  Q4U443

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.214	α = 90
b = 54.642	β = 90
c = 124.152	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
cctbx.xfel	data reduction
cctbx.prime	data scaling
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Lyubimov, A.Y., Mathews, I.I., Uervivojnangkoorn, M., Khosla, C., Soltis, S.M., Cohen, A.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 2.0: 2018-04-11
  Changes: Data collection, Polymer sequence
• Version 2.1: 2018-11-28
  Changes: Data collection
• Version 2.2: 2019-12-04
  Changes: Author supporting evidence
• Version 2.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description