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- EMDB-28615: MicroED structure of an Aeropyrum pernix protoglobin mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-28615
TitleMicroED structure of an Aeropyrum pernix protoglobin mutant
Map data
Sample
  • Complex: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant
    • Protein or peptide: Protogloblin ApPgb
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IMIDAZOLE
  • Ligand: FE (III) ION
  • Ligand: water
KeywordsMicroED / protoglobin / directed evolution / METAL BINDING PROTEIN
Function / homologyProtoglobin / Globin-sensor domain / Protoglobin / Globin/Protoglobin / Globin-like superfamily / oxygen binding / heme binding / Protogloblin ApPgb
Function and homology information
Biological speciesAeropyrum pernix (archaea)
Methodelectron crystallography / cryo EM / Resolution: 2.1 Å
AuthorsDanelius E / Gonen T / Unge JT
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM136508 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To be published
Title: MicroED structure of a protoglobin reactive carbene intermediate
Authors: Danelius E / Porter NJ / Unge J / Arnold FH / Gonen T
History
DepositionOct 18, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28615.png

Downloads & links

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Map

FileDownload / File: emd_28615.map.gz / Format: CCP4 / Size: 25.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX: 0.51372 Å / Y: 0.48558 Å / Z: 0.50459 Å
Density
Contour LevelBy AUTHOR: 1.41858
Minimum - Maximum-3.4921148 - 9.948743
Average (Standard dev.)-0.0057642898 (±0.9483574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin-119-134-90
Dimensions179196190
Spacing190179196
CellA: 97.60764 Å / B: 86.918076 Å / C: 98.899025 Å
α: 104.095 ° / β: 98.5833 ° / γ: 90.109 °

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Supplemental data

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Sample components

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Entire : Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L,...

EntireName: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant
Components
  • Complex: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant
    • Protein or peptide: Protogloblin ApPgb
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: IMIDAZOLE
  • Ligand: FE (III) ION
  • Ligand: water

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Supramolecule #1: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L,...

SupramoleculeName: Homotetramer of Aeropyrum pernix protoglobin (ApePgb) C45G, W59L, Y60V, V63R, C102S, F145Q, I149L mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Aeropyrum pernix (archaea)

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Macromolecule #1: Protogloblin ApPgb

MacromoleculeName: Protogloblin ApPgb / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Aeropyrum pernix (archaea)
Molecular weightTheoretical: 22.187307 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
IPGYDYGRVE KSPITDLEFD LLKKTVMLGE KDVMYLKKAG DVLKDQVDEI LDLLVGWRAS NEHLIYYFSN PDTGEPIKEY LERVRARFG AWILDTTSRD YNREWLDYQY EVGLRHHRSK KGVTDGVRTV PHIPLRYLIA QIYPLTATIK PFLAKKGGSP E DIEGMYNA WFKSVVLQVA IWSHPYTKEN DW

UniProtKB: Protogloblin ApPgb

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #3: IMIDAZOLE

MacromoleculeName: IMIDAZOLE / type: ligand / ID: 3 / Number of copies: 15 / Formula: IMD
Molecular weightTheoretical: 69.085 Da
Chemical component information

ChemComp-IMD:
IMIDAZOLE / Imidazole

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Macromolecule #4: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 308 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron crystallography
Aggregation state3D array

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Sample preparation

Concentration20 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Camera length: 2460 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 77.0 K / Max: 90.0 K
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 0.00025 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Crystallography statisticsNumber intensities measured: 33826 / Number structure factors: 33826 / Fourier space coverage: 72 / R merge: 0.43 / Overall phase residual: 0 / High resolution: 2.1 Å / Shell - Shell ID: 1 / Shell - High resolution: 2.1 Å / Shell - Low resolution: 24.27 Å / Shell - Number structure factors: 33826 / Shell - Phase residual: 21.11 / Shell - Fourier space coverage: 73.1 / Shell - Multiplicity: 4.1
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Software - Name: PHENIX (ver. 1.20.1-4487-000)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Overall B value: 26.51 / Target criteria: maximum likelihood
Output model

PDB-8eum:
MicroED structure of an Aeropyrum pernix protoglobin mutant

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