[English] 日本語
Yorodumi
- PDB-9t0l: Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A reso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9t0l
TitleCatalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution
ComponentsCatalase
KeywordsOXIDOREDUCTASE / Catalase / NADPH / PROTOPORPHYRIN IX CONTAINING FE
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / periplasmic space / heme binding / 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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / 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 immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / 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 speciesAgrobacterium radiobacter (Agrobacterium genomosp. 4)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.73 Å
AuthorsLi, J. / Henderson, R. / Russo, C.J. / Wilson, H. / Chen, S.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
CitationJournal: To Be Published
Title: Comparison of human and bacterial monofunctional catalase structures obtained by electron cryomicroscopy.
Authors: Slowik, D. / Li, J. / Wilson, H. / Shtyrov, A. / Chen, S. / McMullan, G. / Russo, C.J. / Mushudov, G. / Henderson, R.
History
DepositionOct 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4943
Polymers55,1321
Non-polymers1,3622
Water7,656425
1
A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules

A: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,97612
Polymers220,5284
Non-polymers5,4488
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
2generate(-1), (-1), (1)409.60001, 409.60001
3generate(1), (-1), (-1)409.60001, 409.60001
4generate(-1), (1), (-1)409.60001, 409.60001

-
Components

#1: Protein Catalase


Mass: 55131.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium radiobacter (Agrobacterium genomosp. 4)
Strain: 2-1 / Gene: katH / Plasmid: pUCIDT-Amp / Production host: Escherichia coli (E. coli) / References: UniProt: B6EXX7, catalase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Catalase with cofactor NADPH / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.22 MDa / Experimental value: NO
Source (natural)Organism: Agrobacterium radiobacter (Agrobacterium genomosp. 4)
Strain: 2-1 / Cellular location: periplasm
Source (recombinant)Organism: Escherichia coli (E. coli) / Plasmid: pUCIDT-Amp
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1154 mMsodium chlorideNaCl1
210 mMsodium phosphateNaH2PO4-Na2HPO41
30.02 mMNicotinamide adenine diphosphateC21H30N7O17P31
45 mMCHAPSOC32H58N2O8S1
SpecimenConc.: 25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: HexAuFoil
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Details: There were 12 optical groups with AFIS up to 12 microns.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 155000 X / Calibrated magnification: 273437 X / Nominal defocus max: 2250 nm / Nominal defocus min: 1450 nm / Calibrated defocus min: 1450 nm / Calibrated defocus max: 2250 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Temperature (max): 80 K / Temperature (min): 80 K / Residual tilt: 0.67 mradians
Image recordingAverage exposure time: 3 sec. / Electron dose: 50.4 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 35543
Details: Images were collected using AFIS with maximum image shifts of 12 microns.
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

-
Processing

EM software
IDNameVersionCategoryDetails
1Topazparticle selection
2EPUimage acquisition
4RELION4CTF correction
7Coot0.9.8.93model fittingCryo-EM module used to dock the
9RELION4initial Euler assignment
10RELION4final Euler assignment
11RELION4classification
12RELION43D reconstruction
13Servalcat0.4.72model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2071946
Details: 2168 particles picked manually for Topaz training set.
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 1.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 990333 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 1GWE

1gwe


Pdb chain-ID: A / Accession code: 1GWE / Chain residue range: 6-503
Details: The initial model consisted of the complete biological assembly of PDB entry 1GWE minus the bound water molecules.
Pdb chain residue range: 6-503 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0085250633541810.0118346807
ELECTRON MICROSCOPYs_angle_nonh_d1.5754648357271.83169024

+
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