6N99

Xylose isomerase 2F1 variant from Streptomyces sp. F-1

• PDB DOI: https://doi.org/10.2210/pdb6N99/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces sp. F-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-12-01 Released: 2019-12-04 
• Deposition Author(s): Miyamoto, R.Y., Vieira, P.S., Murakami, M.T., Zanphorlin, L.M.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.316 
• R-Value Work: 0.267 
• R-Value Observed: 0.269 

Literature

Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes.

Miyamoto, R.Y., de Sousa, A.S., Vieira, P.S., de Melo, R.R., Scarpassa, J.A., Ramos, C.H.I., Murakami, M.T., Ruller, R., Zanphorlin, L.M.

(2020) Biochim Biophys Acta Gen Subj 1864: 129549-129549

• PubMed: 32035160 
• DOI: https://doi.org/10.1016/j.bbagen.2020.129549
• Primary Citation of Related Structures:  
  6N98, 6N99


• PubMed Abstract: 
  

  Enzymatic isomerization is a promising strategy to solve the problem of xylose fermentation and, consequently, to leverage the production of advanced biofuels and biochemicals. In a previous work, our research group discovered a new strain of Streptomyces with great biotechnological potential due to its ability to produce a broad arsenal of enzymes related to lignocellulose degradation.

---

Organizational Affiliation: 

Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil; Institute of Biology, State University of Campinas, Campinas, SP, Brazil.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 172.31 kDa 
• Atom Count: 12,038 
• Modelled Residue Count: 1,536 
• Deposited Residue Count: 1,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A, B, C, D	388	Streptomyces sp. F-1	Mutation(s): 0  Gene Names: xylA_1, xylA, STEPF1_01030 EC: 5.3.1.5
UniProt
Find proteins for A0A1K2FKX8 (Streptomyces sp. F-1) Explore A0A1K2FKX8  Go to UniProtKB:  A0A1K2FKX8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	J [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4	H [auth B], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth A], F [auth B], G [auth B], K [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.316 
• R-Value Work: 0.267 
• R-Value Observed: 0.269 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.776	α = 90
b = 82.293	β = 109.81
c = 140.313	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Currently 6N99 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-12-04 
Deposition Author(s): Miyamoto, R.Y., Vieira, P.S., Murakami, M.T., Zanphorlin, L.M.

---

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2018/02865-2
Sao Paulo Research Foundation (FAPESP)	Brazil	2016/06509-0

Revision History  

• Version 1.0: 2019-12-04
  Type: Initial release
  
• Version 1.1: 2020-06-03
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description