[English] 日本語
Yorodumi
- PDB-6jnt: Catalase structure determined by eEFD (dataset 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6jnt
TitleCatalase structure determined by eEFD (dataset 1)
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Electron 3D crystallography / eEFD / energy filter / ParallEM / CRYO ARM
Function / homology
Function and homology information


Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / catalase / catalase activity / Neutrophil degranulation / positive regulation of cell division / hydrogen peroxide catabolic process / response to hydrogen peroxide ...Detoxification of Reactive Oxygen Species / catalase complex / cellular detoxification of hydrogen peroxide / Peroxisomal protein import / 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
Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / Catalase haem-binding site / Catalase proximal heme-ligand signature. ...Hemocyanin, N-terminal domain - #60 / Cytochrome C Oxidase; Chain J - #20 / Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Cytochrome C Oxidase; Chain J / Hemocyanin, N-terminal domain / Catalase HpII, Chain A, domain 1 / Catalase core domain / 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 / Few Secondary Structures / Irregular / Up-down Bundle / Beta Barrel / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-NDP / Catalase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3 Å
AuthorsYonekura, K. / Maki-Yonekura, S.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16H04757 Japan
Japan Society for the Promotion of Science24657111 Japan
Japan Agency for Medical Research and Development (AMED)CiCLE Japan
Japan Science and TechnologySENTAN program Japan
CitationJournal: J Struct Biol / Year: 2019
Title: A new cryo-EM system for electron 3D crystallography by eEFD.
Authors: Koji Yonekura / Tetsuya Ishikawa / Saori Maki-Yonekura /
Abstract: A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, ...A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200 kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.
History
DepositionMar 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area54340 Å2
ΔGint-300 kcal/mol
Surface area59920 Å2
Unit cell
Length a, b, c (Å)69.109, 171.901, 195.013
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Bovine catalase / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Source (natural)Organism: Bos taurus (cattle)
Buffer solutionpH: 5.3
Buffer componentName: potassium / sodium phosphate buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

-
Data collection

MicroscopyModel: JEOL CRYO ARM 300 / Date: Sep 26, 2018
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION
Image recordingElectron dose: 2.9 e/Å2 / Film or detector model: OTHER
EM diffractionCamera length: 4659 mm
EM diffraction shellResolution: 3→47.35 Å / Fourier space coverage: 82.6 % / Multiplicity: 2.9 / Num. of structure factors: 38238 / Phase residual: 30.48 °
EM diffraction statsFourier space coverage: 82.6 % / High resolution: 3 Å / Num. of intensities measured: 38238 / Num. of structure factors: 38238 / Phase error: 30.48 ° / Phase residual: 30.48 ° / Phase error rejection criteria: None / Rmerge: 0.251 / Rsym: 0.251
DetectorDate: Sep 26, 2018

-
Processing

SoftwareName: PHENIX / Version: (1.14_3260: ???) / Classification: refinement
EM softwareName: PHENIX / Version: 1.14_3260 / Category: model refinement
Image processingDetails: Gatan OneView
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 69.1 Å / B: 171.9 Å / C: 195 Å / Space group name: P212121 / Space group num: 19
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingSpace: RECIPROCAL
Atomic model buildingPDB-ID: 3NWL

3nwl


Accession code: 3NWL / Source name: PDB / Type: experimental model
RefinementResolution: 3→47.35 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 30.48
RfactorNum. reflection% reflection
Rfree0.283 1984 5.19 %
Rwork0.2508 --
obs0.2526 38238 82.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.00616956
ELECTRON CRYSTALLOGRAPHYf_angle_d0.6523124
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d11.1739912
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.0432328
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.0043068
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.381270.3362364ELECTRON CRYSTALLOGRAPHY76
3.075-3.15810.36141390.30942578ELECTRON CRYSTALLOGRAPHY81
3.1581-3.2510.31911420.30872572ELECTRON CRYSTALLOGRAPHY82
3.251-3.3560.34381430.29542591ELECTRON CRYSTALLOGRAPHY82
3.356-3.47590.35771410.29062607ELECTRON CRYSTALLOGRAPHY82
3.4759-3.6150.29991450.27022645ELECTRON CRYSTALLOGRAPHY82
3.615-3.77940.29011430.2592595ELECTRON CRYSTALLOGRAPHY82
3.7794-3.97860.27541430.24772611ELECTRON CRYSTALLOGRAPHY82
3.9786-4.22770.29671440.24162618ELECTRON CRYSTALLOGRAPHY82
4.2277-4.55390.23281440.21932633ELECTRON CRYSTALLOGRAPHY82
4.5539-5.01170.22011430.21062612ELECTRON CRYSTALLOGRAPHY81
5.0117-5.73590.25691440.20962643ELECTRON CRYSTALLOGRAPHY81
5.7359-7.22250.30431450.21592637ELECTRON CRYSTALLOGRAPHY81
7.2225-47.35550.19591410.22412548ELECTRON CRYSTALLOGRAPHY74
Refinement TLS params.Method: refined / Origin x: 66.0765 Å / Origin y: 70.3035 Å / Origin z: 135.5889 Å
111213212223313233
T0.0728 Å20.0088 Å2-0.0048 Å2-0.0596 Å2-0.0158 Å2--0.1356 Å2
L0.088 °2-0.0122 °20.036 °2-0.0114 °20.0319 °2--0.1208 °2
S0.0018 Å °0.0223 Å °-0.0143 Å °0.0056 Å °-0.0002 Å °0.0044 Å °0.006 Å °-0.0029 Å °0.0287 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more