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- EMDB-55404: Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A reso... -

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Basic information

Entry
Database: EMDB / ID: EMD-55404
TitleCatalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution
Map dataContour level is in Volts
Sample
  • Organelle or cellular component: Catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water
KeywordsCatalase / NADPH / PROTOPORPHYRIN IX CONTAINING FE / OXIDOREDUCTASE
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
Biological speciesAgrobacterium radiobacter (Agrobacterium genomosp. 4)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.73 Å
AuthorsLi J / Henderson R / Russo CJ / Wilson H / Chen S
Funding support United Kingdom, 1 items
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 CJ / Mushudov G / Henderson R
History
DepositionOct 17, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55404.png

Downloads & links

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Map

FileDownload / File: emd_55404.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContour level is in Volts
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å		0.8 Å/pix.
x 512 pix.
= 409.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.026
Minimum - Maximum-0.07073783 - 0.2119914
Average (Standard dev.)0.00003814072 (±0.001773251)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 409.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55404_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55404_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55404_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Catalase with cofactor NADPH

EntireName: Catalase with cofactor NADPH
Components
  • Organelle or cellular component: Catalase with cofactor NADPH
    • Protein or peptide: Catalase
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: water

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Supramolecule #1: Catalase with cofactor NADPH

SupramoleculeName: Catalase with cofactor NADPH / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Agrobacterium radiobacter (Agrobacterium genomosp. 4)
Strain: 2-1 / Location in cell: periplasm
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Catalase

MacromoleculeName: Catalase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: catalase
Source (natural)Organism: Agrobacterium radiobacter (Agrobacterium genomosp. 4)
Strain: 2-1
Molecular weightTheoretical: 55.131996 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTDMNKKQGG TGSTTGTGAP AVSDRNSLTV GPDGPILLHD VHFLEQMAHF NREKVPERQP HAKGSGAFGT FETTHDVSAY TKAALFQKG ATTEMLARFS TVAGEMGSPD TWRDVRGFSL KFYTDEGNYD LVGNNTPIFF VRDPMKFPHF IRSQKRLPDS G LRDNHMQW ...String:
MTDMNKKQGG TGSTTGTGAP AVSDRNSLTV GPDGPILLHD VHFLEQMAHF NREKVPERQP HAKGSGAFGT FETTHDVSAY TKAALFQKG ATTEMLARFS TVAGEMGSPD TWRDVRGFSL KFYTDEGNYD LVGNNTPIFF VRDPMKFPHF IRSQKRLPDS G LRDNHMQW DFWTNNPESA HQVTYLMGVR GLPRTWRHMN GYGSHTYMWV NEAGERFWVK YHFHTHQGME FFTNEEAGAM AG ADADFHR RDLFDAIARG EHPAWTMSVQ VMPYEEGKTY HINPFDLTKT WPHADYPLIE VGKMTLNRNP ENFFAQIEQA AFS PGNTVP GIGLSPDKML LGRAFAYNDA QRNRIGTNFH QLPVNQPKVP VNTYMFDGQM AYHHSGSAPV HATNSGGRSW SDET GAVHD GWEADGDFVR SAYTLRPGDD DFSQPGKLVR EVFNDDERRQ LVETVSGALL GGVRSPVLER AFDYWKSVDA EVGQR IEDA VRAGQAG

UniProtKB: Catalase

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 3 / Number of copies: 1 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 425 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration25 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
154.0 mMNaClsodium chloride
10.0 mMNaH2PO4-Na2HPO4sodium phosphate
0.02 mMC21H30N7O17P3Nicotinamide adenine diphosphate
5.0 mMC32H58N2O8SCHAPSO
GridModel: HexAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 45 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 75 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.003 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 0.67 mrad
DetailsThere were 12 optical groups with AFIS up to 12 microns.
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 35543 / Average exposure time: 3.0 sec. / Average electron dose: 50.4 e/Å2
Details: Images were collected using AFIS with maximum image shifts of 12 microns.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.25 µm / Calibrated defocus min: 1.45 µm / Calibrated magnification: 273437 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 1.45 µm / Nominal magnification: 155000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2071946
Details: 2168 particles picked manually for Topaz training set.
CTF correctionSoftware - Name: RELION (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

13256

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 990333
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 12 / Avg.num./class: 82500 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1gwe


Chain - Chain ID: A / Chain - Residue range: 6-503 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of the complete biological assembly of PDB entry 1GWE minus the bound water molecules.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9t0l:
Catalase CryoEM Structure from Rhizobium radiobacter at 1.7A resolution

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