7DFK | pdb_00007dfk

Crystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb7DFK/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces pseudogriseolus
• Mutation(s): No 


• Deposited: 2020-11-08 Released: 2021-11-17 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of xylitol-bound glucose isomerase by serial millisecond crystallography

Nam, K.H.

To be published.

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 43.46 kDa 
• Atom Count: 3,413 
• Modeled Residue Count: 385 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xylose isomerase	A	388	Streptomyces pseudogriseolus	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYL (Subject of Investigation/LOI)	C [auth A]	Xylitol C5 H12 O5 HEBKCHPVOIAQTA-SCDXWVJYSA-N
MG (Subject of Investigation/LOI)	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.251 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Diffraction Data: https://doi.org/10.11577/1777828

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.138	α = 90
b = 99.936	β = 90
c = 103.156	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystFEL	data reduction
CrystFEL	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Nam, K.H.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017M3A9F6029736
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2017R1D1A1B03033087

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2023-09-06
  Changes: Data collection, Database references
• Version 1.2: 2023-11-29
  Changes: Refinement description