6ISK | pdb_00006isk

SnoaL-like cyclase XimE

• PDB DOI: https://doi.org/10.2210/pdb6ISK/pdb

• Classification: LYASE
• Organism(s): Streptomyces xiamenensis 318
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-11-16 Released: 2019-11-20 
• Deposition Author(s): He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.
• Funding Organization(s): National Natural Science Foundation of China

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis

He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.

(2019) ACS Catal 9: 5391-5399

• DOI: https://doi.org/10.1021/acscatal.9b01034

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.78 kDa 
• Atom Count: 1,935 
• Modeled Residue Count: 240 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
XimE, SnoaL-like domain protein	A, B	158	Streptomyces xiamenensis 318	Mutation(s): 0  Gene Names: ximE EC: 4.2.99
UniProt
Find proteins for U5Q2N8 (Streptomyces xiamenensis) Explore U5Q2N8  Go to UniProtKB:  U5Q2N8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA (Subject of Investigation/LOI)	C [auth A], D [auth A], F [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
EDO (Subject of Investigation/LOI)	E [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.894	α = 90
b = 79.894	β = 90
c = 111.721	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): He, B., Zhou, T., Bu, X., Weng, J., Xu, J., Lin, S., Zheng, J., Zhao, Y., Xu, M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81473105

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references
• Version 1.2: 2024-03-27
  Changes: Data collection, Database references