+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32974 | |||||||||
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Title | Capsid structure of Staphylococcus jumbo bacteriophage S6 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Phage / Phage head / CryoEM / Virus / Bacteriophage / Cryo-EM | |||||||||
Biological species | Staphylococcus phage S6 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Koibuchi W / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: To Be Published Title: Capsid structure of Staphylococcus jumbo bacteriophage S6 Authors: Koibuchi W / Uchiyama J / Matsuzaki S / Murata K / Iwasaki K / Miyazaki N | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32974.map.gz | 427.5 MB | EMDB map data format | |
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Header (meta data) | emd-32974-v30.xml emd-32974.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32974_fsc.xml | 28.6 KB | Display | FSC data file |
Images | emd_32974.png | 240.9 KB | ||
Filedesc metadata | emd-32974.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32974 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32974 | HTTPS FTP |
-Validation report
Summary document | emd_32974_validation.pdf.gz | 626.1 KB | Display | EMDB validaton report |
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Full document | emd_32974_full_validation.pdf.gz | 625.7 KB | Display | |
Data in XML | emd_32974_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | emd_32974_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32974 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32974 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32974.map.gz / Format: CCP4 / Size: 2.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.7 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Staphylococcus phage S6
Entire | Name: Staphylococcus phage S6 (virus) |
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Components |
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-Supramolecule #1: Staphylococcus phage S6
Supramolecule | Name: Staphylococcus phage S6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2913378 / Sci species name: Staphylococcus phage S6 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / Name: Head / Diameter: 1300.0 Å / T number (triangulation number): 27 |
-Macromolecule #1: Major structural protein ORF12
Macromolecule | Name: Major structural protein ORF12 / type: protein_or_peptide / ID: 1 / Number of copies: 27 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage S6 (virus) |
Molecular weight | Theoretical: 59.259133 KDa |
Sequence | String: MLNPNRIKDE FSVRLEDIEN SINESYNLST IGGDFAAIAT DDAVFESYKD QLLEGFDAAE GEALAGMLDN TREEILMESS MGPIQPYAS LSMPILVKLW ARLALTEALP TQVANKPNFT VPILTPYVVD ADGNKHALPE SINNTPETLV GLVQIKEDIA V EGGKVTDY ...String: MLNPNRIKDE FSVRLEDIEN SINESYNLST IGGDFAAIAT DDAVFESYKD QLLEGFDAAE GEALAGMLDN TREEILMESS MGPIQPYAS LSMPILVKLW ARLALTEALP TQVANKPNFT VPILTPYVVD ADGNKHALPE SINNTPETLV GLVQIKEDIA V EGGKVTDY DLFTGLKEGK EVRKGIDRLD RKFKIVEAKW SDSFDERTSA AGFVELGSNV VKLQDNDTLV GQIKYPTNGD GE VETDTIL GKVDVSSGEL TLTSASGKLT DVKVKGYVAS EQHTSATNVE LGLTRKDVVI DTAQHIEATV PLEVIQDMKA TYD IDGVAR LSETMSQLSS QKVDLDIIEF LDHEYKETDA KYHFSFDVFP HSDYSAHPKD WLEGLREVID HTTQSMKNDY KLYD VQFVI VGNPLDVRLI PNVSWTFNGG DRNADAYSNG IKINYSLGAA SGTANYRIIG SDLVRQGELT IIAIPQQDNY KTFMF YPYT FNVVNGGGYL NTRNPNVPNM MMTRRYTVES FVPIIGRITI KNNNGSVYAR |
-Macromolecule #2: Hoc-like protein ORF90
Macromolecule | Name: Hoc-like protein ORF90 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylococcus phage S6 (virus) |
Molecular weight | Theoretical: 53.151375 KDa |
Sequence | String: MATTNYFKVK LLDEKLIPFL GLGERGPREN VILSSNDLAS LKQAGWTVTD VQPLPETGKI KYDRRTVYFK SEGETGKFIN VPFYINPVD ARDVLGLLKF DLIKLSDKSV VKTYTAKDIK SEILSLPTSD LEVNEEYELK LYFPKDASEN YDIAISEGHK N LFERVKDS ...String: MATTNYFKVK LLDEKLIPFL GLGERGPREN VILSSNDLAS LKQAGWTVTD VQPLPETGKI KYDRRTVYFK SEGETGKFIN VPFYINPVD ARDVLGLLKF DLIKLSDKSV VKTYTAKDIK SEILSLPTSD LEVNEEYELK LYFPKDASEN YDIAISEGHK N LFERVKDS VFIKVKEYGK FTGRLVQLQQ DINVLKESAL PLDKILGYKD FDTKEVTPVA KENLLQLLSV NVSDESYARY QA DKNRLLF FSKTGEILVK VIERSIQDNI VNFNIRILDE ETIQNEIDKK IEYSVYDPKD GKFESINQTK SITVTPETVN IEA EQTQKL EVTTEPEGRK VSFELKDGSE FASVDNNGNI TGISEGTANV TVKSDDVSKN VEVNVSRLKT KSLTVTPEEV NIDA ESTQQ LDVKIQPSTN SVSYSITEGS EYASVNNSGL VTAKAAGTAK VKVTSDSVSK DVSVTISTSQ VEETPEETTT E |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |