6QNI | pdb_00006qni

Liquid Application Method for time-resolved Analyses (LAMA) by serial synchrotron crystallography, Xylose Isomerase 1.0 s timepoint

• PDB DOI: https://doi.org/10.2210/pdb6QNI/pdb

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


• Deposited: 2019-02-11 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: 1.85 Å
• R-Value Free: 
  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.165 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Literature

Liquid application method for time-resolved analyses by serial synchrotron crystallography.

Mehrabi, P., Schulz, E.C., Agthe, M., Horrell, S., Bourenkov, G., von Stetten, D., Leimkohl, J.P., Schikora, H., Schneider, T.R., Pearson, A.R., Tellkamp, F., Miller, R.J.D.

(2019) Nat Methods 16: 979-982

• PubMed: 31527838 
• DOI: https://doi.org/10.1038/s41592-019-0553-1
• Primary Citation Related Structures: 
  6QNB, 6QNC, 6QND, 6QNH, 6QNI, 6QNJ, 6RNB, 6RNC, 6RND, 6RNF


• PubMed Abstract: 
  

  We introduce a liquid application method for time-resolved analyses (LAMA), an in situ mixing approach for serial crystallography. Picoliter-sized droplets are shot onto chip-mounted protein crystals, achieving near-full ligand occupancy within theoretical diffusion times. We demonstrate proof-of-principle binding of GlcNac to lysozyme, and resolve glucose binding and subsequent ring opening in a time-resolved study of xylose isomerase.

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Organizational Affiliation: 
• Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany.
Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany.
Institute for Nanostructure and Solid State Physics, Universität Hamburg, Hamburg, Germany.
European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen Synchrotron, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Scientific Support Unit Machine Physics, Hamburg, Germany.
Max-Planck-Institute for Structure and Dynamics of Matter, Department for Atomically Resolved Dynamics, Hamburg, Germany. [e-mail].
Centre for Ultrafast Imaging, Universität Hamburg, Hamburg, Germany. [e-mail].
University of Toronto, Departments of Chemistry and Physics, Toronto, Ontario, Canada. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.55 kDa 
• Atom Count: 3,358 
• Modeled 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 pseudogriseolus	Mutation(s): 0  Gene Names: xylA EC: 5.3.1.5
UniProt
Find proteins for P24300 (Streptomyces pseudogriseolus) Explore P24300  Go to UniProtKB:  P24300

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
CO	D [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.196 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.165 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.62	α = 90
b = 99.38	β = 90
c = 87.63	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	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: 2019-11-20
  Changes: Derived calculations, Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-05-15
  Changes: Data collection, Database references, Structure summary