5K7T

MicroED structure of thermolysin at 2.5 A resolution


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
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolysin316Bacillus thermoproteolyticusMutation(s): 0 
EC: 3.4.24.27
UniProt
Find proteins for P00800 (Bacillus thermoproteolyticus)
Explore P00800 
Go to UniProtKB:  P00800
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00800
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DMS
Query on DMS

Download Ideal Coordinates CCD File 
G [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
H [auth A]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.065α = 90
b = 92.065β = 90
c = 128.498γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.10_2155

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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