6KD2

Room temperature structure of glucose isomerase delivered in gelatin by serial millisecond crystallography

• PDB DOI: https://doi.org/10.2210/pdb6KD2/pdb

• Classification: ISOMERASE
• Organism(s): Streptomyces rubiginosus
• Expression System: Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2019-06-30 Released: 2019-07-17 
• Deposition Author(s): Nam, K.H.
• Funding Organization(s): National Research Foundation (Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 

Literature

Stable sample delivery in viscous media via a capillary for serial crystallography.

Nam, K.H.

(2020) J Appl Crystallogr 53: 45-50

• DOI: https://doi.org/10.1107/S1600576719014985

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: 43.33 kDa 
• Atom Count: 3,347 
• Modelled Residue Count: 386 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.224 
• R-Value Work: 0.193 
• R-Value Observed: 0.193 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.52	α = 90
b = 100.17	β = 90
c = 103.57	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: 2019-07-17 
Deposition Author(s): Nam, K.H.

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

Revision History  

• Version 1.0: 2019-07-17
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection
• Version 1.2: 2019-09-18
  Changes: Data collection
• Version 1.3: 2020-07-29
  Changes: Database references
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Refinement description