9BDJ | pdb_00009bdj

MicroED structure of bovine liver catalase with missing cone eliminated by suspended drop

  • Classification: OXIDOREDUCTASE
  • Organism(s): Bos taurus
  • Mutation(s): No 

  • Deposited: 2024-04-11 Released: 2024-09-18 
  • Deposition Author(s): Gillman, C., Bu, G., Gonen, T.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Defense (DOD, United States), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 4.00 Å
  • R-Value Free: 
    0.358 (Depositor) 
  • R-Value Work: 
    0.317 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Eliminating the missing cone challenge through innovative approaches.

Gillman, C.Bu, G.Danelius, E.Hattne, J.Nannenga, B.L.Gonen, T.

(2024) J Struct Biol X 9: 100102-100102

  • DOI: https://doi.org/10.1016/j.yjsbx.2024.100102
  • Primary Citation of Related Structures:  
    8VD7, 9BDJ

  • PubMed Abstract: 

    Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.


  • Organizational Affiliation
    • Department of Biological Chemistry, University of California, Los Angeles, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase
A, B, C, D
527Bos taurusMutation(s): 0 
EC: 1.11.1.6
UniProt
Find proteins for P00432 (Bos taurus)
Explore P00432 
Go to UniProtKB:  P00432
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00432
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP (Subject of Investigation/LOI)
Query on NDP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 4.00 Å
  • R-Value Free:  0.358 (Depositor) 
  • R-Value Work:  0.317 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.65α = 90
b = 173.3β = 90
c = 182.78γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM136508
Department of Defense (DOD, United States)United StatesHDTRA1-21-1-0004
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary