5K7P

MicroED structure of xylanase at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5K7P/pdb
• EM Map EMD-8218: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Mutation(s): No 


• Deposited: 2016-05-26 Released: 2017-04-05 
• Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 

Literature

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.

de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Weiss, S.C., Kim, S.K., Hinck, C.S., Hinck, A.P., Calero, G., Eisenberg, D., Gonen, T.

(2017) Nat Methods 14: 399-402

• PubMed: 28192420 
• DOI: https://doi.org/10.1038/nmeth.4178
• Primary Citation of Related Structures:  
  5K7N, 5K7O, 5K7P, 5K7Q, 5K7R, 5K7S, 5K7T, 5TY4


• PubMed Abstract: 
  

  Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA.

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: 21.11 kDa 
• Atom Count: 1,506 
• Modelled Residue Count: 190 
• Deposited Residue Count: 190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-xylanase 2	A	190	Trichoderma reesei	Mutation(s): 0  EC: 3.2.1.8
UniProt
Find proteins for P36217 (Hypocrea jecorina (strain ATCC 56765 / BCRC 32924 / NRRL 11460 / Rut C-30)) Explore P36217  Go to UniProtKB:  P36217

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	B [auth A], C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.30 Å
• R-Value Free: 0.267 
• R-Value Work: 0.230 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data: https://doi.org/10.15785/SBGRID/286

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.161	α = 90
b = 59.752	β = 90
c = 69.812	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10_2155

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2018-08-22
  Changes: Data collection, Database references
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Refinement description