+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33598 | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp7 icosahedral head | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Podophage / icosahedral head / VIRUS | |||||||||
Biological species | Klebsiella phage Kp7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Huang L / Xiang Y | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Structure and assembly of the Klebsiella pneumoniae phage tail fibers Authors: Huang L / Xiang Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33598.map.gz | 386.2 MB | EMDB map data format | |
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Header (meta data) | emd-33598-v30.xml emd-33598.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33598_fsc.xml | 35.2 KB | Display | FSC data file |
Images | emd_33598.png | 20.7 KB | ||
Filedesc metadata | emd-33598.cif.gz | 5.1 KB | ||
Others | emd_33598_half_map_1.map.gz emd_33598_half_map_2.map.gz | 3 GB 3 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33598 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33598 | HTTPS FTP |
-Validation report
Summary document | emd_33598_validation.pdf.gz | 915.3 KB | Display | EMDB validaton report |
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Full document | emd_33598_full_validation.pdf.gz | 914.9 KB | Display | |
Data in XML | emd_33598_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | emd_33598_validation.cif.gz | 57.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33598 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33598 | HTTPS FTP |
-Related structure data
Related structure data | 7y3tMC 7xy1C 7xycC 7y1cC 7y22C 7y23C 7y5sC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33598.map.gz / Format: CCP4 / Size: 3.7 GB / 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: 1.17 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33598_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33598_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Klebsiella phage Kp7
Entire | Name: Klebsiella phage Kp7 (virus) |
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Components |
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-Supramolecule #1: Klebsiella phage Kp7
Supramolecule | Name: Klebsiella phage Kp7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2936515 / Sci species name: Klebsiella phage Kp7 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Klebsiella pneumoniae ATCC 43816 (bacteria) |
Virus shell | Shell ID: 1 / Diameter: 600.0 Å / T number (triangulation number): 7 |
-Macromolecule #1: phage major capsid protein
Macromolecule | Name: phage major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp7 (virus) |
Molecular weight | Theoretical: 39.74375 KDa |
Sequence | String: MSTPNVLTNV AVSHSGEVDS LLIEKFNGKV REQYLKGENL LSHFQVETVT GTNTVSNKYL GETEIQVLAP GQSPAATPTK ADKNQVVID TTVIARNTVA MLHDVQGDID SLKPKIAVNQ AKQLKRLEDE MVVQQLMLGG ISNTKAQRTN PRVPGHGFSI N VNITADTA ...String: MSTPNVLTNV AVSHSGEVDS LLIEKFNGKV REQYLKGENL LSHFQVETVT GTNTVSNKYL GETEIQVLAP GQSPAATPTK ADKNQVVID TTVIARNTVA MLHDVQGDID SLKPKIAVNQ AKQLKRLEDE MVVQQLMLGG ISNTKAQRTN PRVPGHGFSI N VNITADTA ETSPQYLAAA IEYALEQQLE QEVDISDLVI LMPWKFFNAL RDMDRIVDRS YTLADESTVQ GFALKSFNVP VV PSNRFPK FSQGAAHHKL SNADNGFRYD TTAPMAGAVA VIFSMDALLV GRTIELTGDI FWEKKEKTFY IDTYLAEGAI PDR WEAVSV VTTARNATTG DPDGTGADDT VVTKRANRKV ILTKAVS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |