5K7T

MicroED structure of thermolysin at 2.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5K7T/pdb
• EM Map EMD-8222: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Bacillus thermoproteolyticus
• 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: 2.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.290 
• R-Value Observed: 0.291 

Starting Model: experimental

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: 34.72 kDa 
• Atom Count: 2,466 
• Modelled Residue Count: 316 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thermolysin	A	316	Bacillus thermoproteolyticus	Mutation(s): 0  EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus) Explore P00800  Go to UniProtKB:  P00800

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMS	G [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	H [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.50 Å
• R-Value Free: 0.310 
• R-Value Work: 0.290 
• R-Value Observed: 0.291 
• Space Group: P 6₁ 2 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/290

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.065	α = 90
b = 92.065	β = 90
c = 128.498	γ = 120

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