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Yorodumi- EMDB-15691: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15691 | |||||||||
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Title | Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Heme A synthase / Oligomerization / Function / Heme A / MEMBRANE PROTEIN | |||||||||
Function / homology | COX15/CtaA family / Cytochrome oxidase assembly protein / oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor / heme A biosynthetic process / membrane / Heme O oxygenase Function and homology information | |||||||||
Biological species | Aquifex aeolicus VF5 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Hui Z / Guoliang Z | |||||||||
Funding support | China, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of heme A synthase trimer from Aquifex aeolicus Authors: Hui Z / Guoliang Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15691.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-15691-v30.xml emd-15691.xml | 15.3 KB 15.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15691_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_15691.png | 53.2 KB | ||
Masks | emd_15691_msk_1.map | 64 MB | Mask map | |
Others | emd_15691_half_map_1.map.gz emd_15691_half_map_2.map.gz | 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15691 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15691 | HTTPS FTP |
-Validation report
Summary document | emd_15691_validation.pdf.gz | 677.1 KB | Display | EMDB validaton report |
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Full document | emd_15691_full_validation.pdf.gz | 676.7 KB | Display | |
Data in XML | emd_15691_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | emd_15691_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15691 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15691 | HTTPS FTP |
-Related structure data
Related structure data | 8aw5MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15691.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15691_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15691_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15691_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Heme A synthase with cofactor Heme B
Entire | Name: Heme A synthase with cofactor Heme B |
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Components |
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-Supramolecule #1: Heme A synthase with cofactor Heme B
Supramolecule | Name: Heme A synthase with cofactor Heme B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Aquifex aeolicus VF5 (bacteria) |
-Macromolecule #1: Heme O oxygenase
Macromolecule | Name: Heme O oxygenase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Aquifex aeolicus VF5 (bacteria) / Strain: VF5 |
Molecular weight | Theoretical: 34.984523 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GMNTNLKSSP LKTLVLASVV LTYVLMVFGG IVTSTGSGLG CPDWPLCHGQ LLPFQLKEQI PTPPAPVVAP TPLQPWIEQT HRILGGITG IVLLATLFYA FKRGTSFVKK ALVFIFIALI LEALLGMRVV ITEAPLLREL LHYVYTSAHL ILSVFILSTI T ITYYYVKF ...String: GMNTNLKSSP LKTLVLASVV LTYVLMVFGG IVTSTGSGLG CPDWPLCHGQ LLPFQLKEQI PTPPAPVVAP TPLQPWIEQT HRILGGITG IVLLATLFYA FKRGTSFVKK ALVFIFIALI LEALLGMRVV ITEAPLLREL LHYVYTSAHL ILSVFILSTI T ITYYYVKF FGERPKEYIP YADALYVATM FQILLGIFVR YVKALEYNQF VYYLHITYAG FLVILSLFIM FKEFNKYSLI TF LLMTAQI LAGVATVISG FFLPYLFLHI AIGFFIVLWV SYLVAPSVLK TYTEFRGELA RNSSAWSHPQ FEK UniProtKB: Heme O oxygenase |
-Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE
Macromolecule | Name: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 3 / Formula: HEM |
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Molecular weight | Theoretical: 616.487 Da |
Chemical component information | ChemComp-HEM: |
-Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...
Macromolecule | Name: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate type: ligand / ID: 3 / Number of copies: 9 / Formula: POV |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-POV: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | 3D array |
-Sample preparation
Concentration | 3.5 mg/mL | |||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Homemade / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 165000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |