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- PDB-9bdj: MicroED structure of bovine liver catalase with missing cone elim... -

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Basic information

Entry
Database: PDB / ID: 9bdj
TitleMicroED structure of bovine liver catalase with missing cone eliminated by suspended drop
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Heme-containing enzyme
Function / homology
Function and homology information


catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / peroxisomal matrix / hydrogen peroxide catabolic process ...catalase complex / Detoxification of Reactive Oxygen Species / Peroxisomal protein import / cellular detoxification of hydrogen peroxide / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / peroxisomal matrix / hydrogen peroxide catabolic process / response to hydrogen peroxide / peroxisome / heme binding / enzyme binding / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase active site / Catalase proximal active site signature. / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / MOLECULAR REPLACEMENT / cryo EM / Resolution: 4 Å
AuthorsGillman, C. / Bu, G. / Gonen, T.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
Department of Defense (DOD, United States)HDTRA1-21-1-0004 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J Struct Biol X / Year: 2024
Title: Eliminating the missing cone challenge through innovative approaches.
Authors: Cody Gillman / Guanhong Bu / Emma Danelius / Johan Hattne / Brent L Nannenga / Tamir Gonen /
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 ...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.
History
DepositionApr 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Catalase
B: Catalase
C: Catalase
D: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,44412
Polymers239,9974
Non-polymers5,4488
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54490 Å2
ΔGint-316 kcal/mol
Surface area62680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.650, 173.300, 182.780
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Catalase


Mass: 59999.160 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: from bovine liver / Source: (natural) Bos taurus (cattle) / References: UniProt: P00432, catalase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Bovine liver catalase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 6.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Data collection

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: DIFFRACTION / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 0.0025 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM diffractionCamera length: 2941 mm
EM diffraction shell
Resolution (Å)IDEM diffraction stats-IDFourier space coverage (%)MultiplicityNum. of structure factorsPhase residual (°)
7.26-44.1091191.24.44289648.3
5.77-7.262195.44.89293243.79
5.04-5.773195.85289034.14
4.58-5.044195.85.06284929.38
4.25-4.585195.95.06287933.95
4-4.256196.15.07284942.22
EM diffraction statsFourier space coverage: 94.859 % / High resolution: 4 Å / Num. of intensities measured: 89263 / Num. of structure factors: 18157 / Phase error rejection criteria: Rfree / Rmerge: 65.2

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
EM software
IDNameCategory
8MOLREPmolecular replacement
13REFMACmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 68.65 Å / B: 173.3 Å / C: 182.78 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 4 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→44.109 Å / Cor.coef. Fo:Fc: 0.697 / Cor.coef. Fo:Fc free: 0.696 / SU B: 180.898 / SU ML: 2.445 / Cross valid method: FREE R-VALUE / ESU R Free: 1.443
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.358 855 4.709 %
Rwork0.3166 17300 -
all0.319 --
obs-18155 94.859 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 42.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.648 Å2-0 Å20 Å2
2---6.07 Å20 Å2
3---6.718 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON CRYSTALLOGRAPHYr_bond_refined_d0.0040.01216956
ELECTRON CRYSTALLOGRAPHYr_bond_other_d00.01615232
ELECTRON CRYSTALLOGRAPHYr_angle_refined_deg1.0391.69323124
ELECTRON CRYSTALLOGRAPHYr_angle_other_deg0.3551.59835048
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_1_deg6.13951992
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_2_deg4.0485144
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_other_2_deg1.23658
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_3_deg14.941102596
ELECTRON CRYSTALLOGRAPHYr_dihedral_angle_6_deg14.42210884
ELECTRON CRYSTALLOGRAPHYr_chiral_restr0.0470.22336
ELECTRON CRYSTALLOGRAPHYr_gen_planes_refined0.0040.0220460
ELECTRON CRYSTALLOGRAPHYr_gen_planes_other0.0030.024248
ELECTRON CRYSTALLOGRAPHYr_nbd_refined0.190.22981
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_other0.2050.213370
ELECTRON CRYSTALLOGRAPHYr_nbtor_refined0.1770.28004
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbtor_other0.0740.28305
ELECTRON CRYSTALLOGRAPHYr_xyhbond_nbd_refined0.1680.2310
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_other0.0280.24
ELECTRON CRYSTALLOGRAPHYr_symmetry_nbd_refined0.2290.227
ELECTRON CRYSTALLOGRAPHYr_nbd_other0.2730.299
ELECTRON CRYSTALLOGRAPHYr_symmetry_xyhbond_nbd_refined0.2710.26
ELECTRON CRYSTALLOGRAPHYr_mcbond_it1.6834.1917980
ELECTRON CRYSTALLOGRAPHYr_mcbond_other1.6834.1917980
ELECTRON CRYSTALLOGRAPHYr_mcangle_it3.0367.5469968
ELECTRON CRYSTALLOGRAPHYr_mcangle_other3.0367.5479969
ELECTRON CRYSTALLOGRAPHYr_scbond_it1.3984.3368976
ELECTRON CRYSTALLOGRAPHYr_scbond_other1.3984.3368974
ELECTRON CRYSTALLOGRAPHYr_scangle_it2.6577.94113156
ELECTRON CRYSTALLOGRAPHYr_scangle_other2.6577.94113157
ELECTRON CRYSTALLOGRAPHYr_lrange_it5.09940.71717981
ELECTRON CRYSTALLOGRAPHYr_lrange_other5.09940.71817982
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
4-4.1030.411620.3512420.35313560.820.87296.16520.353
4.103-4.2140.384550.33412360.33713480.8850.89195.77150.335
4.214-4.3350.337630.29212130.29413260.9190.91796.22930.286
4.335-4.4670.319580.30111330.30212420.9340.91295.89370.296
4.467-4.6120.394570.30111290.30612410.8780.91695.56810.294
4.612-4.7720.322600.29310930.29512020.9120.92495.92350.292
4.772-4.950.33460.26910660.27111610.9240.93195.77950.264
4.95-5.150.322510.28610040.28811050.9140.92195.47510.282
5.15-5.3750.322510.2759810.27710770.9250.92795.82170.271
5.375-5.6330.356490.2869340.2910260.9060.9295.8090.285
5.633-5.9330.3380.2819010.2829830.9290.92195.52390.274
5.933-6.2860.428380.3168660.3219450.830.90495.66140.313
6.286-6.710.313270.3088150.3088830.910.90995.35670.303
6.71-7.2340.382280.3217570.3238240.8470.90195.2670.315
7.234-7.9030.326430.326920.327730.8970.90395.08410.332
7.903-8.80.398390.3596180.3616970.8710.86994.26110.361
8.8-10.0950.344310.3365680.3376340.8880.88794.47950.327
10.095-12.2050.373270.374800.375440.8770.88693.19850.381
12.205-16.6350.435190.3953470.3974440.9080.82382.43240.416
16.635-44.1090.487130.5932250.5853000.7770.52379.33330.886

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