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- PDB-7di8: Electron crystallographic structure of Catalase using a direct el... -

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Basic information

Entry
Database: PDB / ID: 7di8
TitleElectron crystallographic structure of Catalase using a direct electron detector at 300 kV
ComponentsCatalase
KeywordsOXIDOREDUCTASE / electron 3d crystallography / direct detector / cryo arm / parallem
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 / hydrogen peroxide catabolic process / response to hydrogen peroxide ...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 / 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 / Resolution: 3.2 Å
AuthorsTakaba, K. / Maki-Yonekura, S. / Yonekura, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24657111 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Front Mol Biosci / Year: 2020
Title: Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector.
Authors: Kiyofumi Takaba / Saori Maki-Yonekura / Satoru Inoue / Tatsuo Hasegawa / Koji Yonekura /
Abstract: Electron 3D crystallography can reveal the atomic structure from undersized crystals of various samples owing to the strong scattering power of electrons. Here, a direct electron detector DE64 was ...Electron 3D crystallography can reveal the atomic structure from undersized crystals of various samples owing to the strong scattering power of electrons. Here, a direct electron detector DE64 was tested for small and thin crystals of protein and an organic molecule using a JEOL CRYO ARM 300 electron microscope. The microscope is equipped with a cold-field emission gun operated at an accelerating voltage of 300 kV, quad condenser lenses for parallel illumination, an in-column energy filter, and a stable rotational goniometer stage. Rotational diffraction data were collected in an unsupervised manner from crystals of a heme-binding enzyme catalase and a representative organic semiconductor material Ph-BTBT-C10. The structures were determined by molecular replacement for catalase and by the direct method for Ph-BTBT-C10. The analyses demonstrate that the system works well for electron 3D crystallography of these molecules with less damaging, a smaller point spread, and less noise than using the conventional scintillator-coupled camera.
History
DepositionNov 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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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
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area52720 Å2
ΔGint-299 kcal/mol
Surface area62250 Å2
Unit cell
Length a, b, c (Å)69.980, 174.020, 199.450
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 genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CAT / Production host: 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: obtained synthetically / 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
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY / Number of used crystals: 1
EM experimentAggregation state: TISSUE / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: Catalase / Type: TISSUE / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 5.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO
Crystal growMethod: batch mode / pH: 5.3

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Data collection

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 0.0025 e/Å2 / Detector mode: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k)
EM diffractionCamera length: 4036 mm
EM diffraction shellResolution: 3.2→131.24 Å / Fourier space coverage: 82.15 % / Multiplicity: 43.6 / Num. of structure factors: 33768 / Phase residual: 33.13 °
EM diffraction statsFourier space coverage: 82.15 % / High resolution: 3.2 Å / Num. of intensities measured: 1783075 / Num. of structure factors: 33768 / Phase error: 33.13 ° / Phase residual: 33.13 ° / Phase error rejection criteria: None / Rmerge: 1.17 / Rsym: 1.17
Diffraction sourceWavelength: 0.0197 Å
DetectorDate: Aug 26, 2020
RadiationMonochromatic (M) / Laue (L): M / Scattering type: electron
Radiation wavelengthWavelength: 0.0197 Å / Relative weight: 1
ReflectionResolution: 3→131.126 Å / Num. obs: 40941 / % possible obs: 82.3 % / Redundancy: 43.552 % / Biso Wilson estimate: 8.65 Å2 / CC1/2: 0.688 / Rmerge(I) obs: 1.159 / Rrim(I) all: 1.173 / Χ2: 0.601 / Net I/σ(I): 3.79 / Num. measured all: 1783075 / Scaling rejects: 58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3-3.1842.1941.7861.9275487789365290.1851.80882.7
3.18-3.443.6031.5372.38267898744261440.2691.55682.6
3.4-3.6744.0611.2982.99252335693557270.4591.31382.6
3.67-4.0243.9351.0783.87232638643152950.6071.09182.3
4.02-4.544.2840.9154.96215488592448660.6960.92682.1
4.5-5.244.4390.8245.68190733520942920.7560.83482.4
5.2-6.3643.940.9324.68158886439936160.6720.94382.2
6.36-943.220.9264.57122357347728310.6520.93781.4
9-131.12640.9830.5577.5467253203016410.9410.56680.8

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 70 Å / B: 174.2 Å / C: 199.5 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER
RefinementResolution: 3.2→131.126 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 33.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3482 1651 4.89 %
Rwork0.3089 32117 -
obs0.3109 33768 82.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.46 Å2 / Biso mean: 16.7903 Å2 / Biso min: 0.22 Å2
Refinement stepCycle: final / Resolution: 3.2→131.13 Å
LigandSolventTotal
Num. atoms588 0 32035
Biso mean31.34 --
Num. residues--1996
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00416956
ELECTRON CRYSTALLOGRAPHYf_angle_d0.73123124
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0452328
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0053068
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d15.1586192
LS refinement shell

Refine-ID: ELECTRON CRYSTALLOGRAPHY / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2-3.29420.36271360.3328263182
3.2942-3.40050.38031350.3318262382
3.4005-3.52210.42671360.3156265082
3.5221-3.66310.3811370.3135265883
3.6631-3.82990.32741360.3048264582
3.8299-4.03180.31171360.3135265283
4.0318-4.28440.3621360.3114266382
4.2844-4.61520.35581380.2985267382
4.6152-5.07970.3281380.2952269582
5.0797-5.81470.30251390.2999270082
5.8147-7.32590.31671380.3048270082
7.3259-131.1260.32491460.2891282781
Refinement TLS params.Method: refined / Origin x: 66.9074 Å / Origin y: 71.125 Å / Origin z: 138.747 Å
111213212223313233
T-0.0103 Å20.0234 Å2-0.0178 Å2--0.0073 Å2-0.0189 Å2--0.0129 Å2
L-0.0012 °20.002 °20.0124 °2-0.0008 °20.0115 °2--0.0048 °2
S-0.012 Å °0.0149 Å °0.0028 Å °-0 Å °0.0097 Å °0.0118 Å °0.0163 Å °-0.0173 Å °0.0713 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1ELECTRON CRYSTALLOGRAPHY1allA3 - 528
2ELECTRON CRYSTALLOGRAPHY1allB3 - 528
3ELECTRON CRYSTALLOGRAPHY1allC3 - 528
4ELECTRON CRYSTALLOGRAPHY1allD3 - 528

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