4J4K

Crystal structure of glucose isomerase

• PDB DOI: https://doi.org/10.2210/pdb4J4K/pdb

• Classification: HYDROLASE
• Organism(s): Streptomyces rubiginosus
• Mutation(s): No 


• Deposited: 2013-02-07 Released: 2014-04-30 
• Deposition Author(s): Kim, M.K., An, Y.J., Lee, S., Jeong, C.S., Cha, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.163 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

Crystal structure of glucose isomerase

Kim, M.K., An, Y.J., Lee, S., Jeong, C.S., Cha, S.S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.9 kDa 
• Atom Count: 3,518 
• Modelled 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 rubiginosus	Mutation(s): 0  EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces rubiginosus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	B [auth A], C [auth A], D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.163 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.927	α = 90
b = 98.867	β = 90
c = 102.638	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-30 
Deposition Author(s): Kim, M.K., An, Y.J., Lee, S., Jeong, C.S., Cha, S.S.

Revision History  

• Version 1.0: 2014-04-30
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations