6RND

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 15 ms timepoint

• PDB DOI: https://doi.org/10.2210/pdb6RND/pdb

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


• Deposited: 2019-05-08 Released: 2019-10-02 
• Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.211 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 

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)

Macromolecule Content

• Total Structure Weight: 43.51 kDa 
• Atom Count: 3,320 
• Modelled Residue Count: 387 
• 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC (Subject of Investigation/LOI)	D [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
MG (Subject of Investigation/LOI)	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: 0.211 
• R-Value Work: 0.164 
• R-Value Observed: 0.167 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.6	α = 90
b = 99.4	β = 90
c = 87.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-10-02 
Deposition Author(s): Mehrabi, P., Schulz, E.C., Miller, R.J.D.

Revision History  

• Version 1.0: 2019-10-02
  Type: Initial release
  
• Version 1.1: 2019-10-09
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-01-24
  Changes: Data collection, Database references, Refinement description, Structure summary