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Yorodumi- EMDB-33623: CryoEM structure of Klebsiella phage Kp7 type I tail fiber gp51 i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33623 | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp7 type I tail fiber gp51 in vitro | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Phage type I tail fiber / VIRAL PROTEIN | |||||||||
Biological species | Klebsiella phage Kp7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 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_33623.map.gz | 26.9 MB | EMDB map data format | |
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Header (meta data) | emd-33623-v30.xml emd-33623.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33623_fsc.xml | 7.1 KB | Display | FSC data file |
Images | emd_33623.png | 19.3 KB | ||
Filedesc metadata | emd-33623.cif.gz | 5.5 KB | ||
Others | emd_33623_half_map_1.map.gz emd_33623_half_map_2.map.gz | 23.5 MB 23.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33623 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33623 | HTTPS FTP |
-Validation report
Summary document | emd_33623_validation.pdf.gz | 686.1 KB | Display | EMDB validaton report |
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Full document | emd_33623_full_validation.pdf.gz | 685.6 KB | Display | |
Data in XML | emd_33623_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_33623_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33623 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33623 | HTTPS FTP |
-Related structure data
Related structure data | 7y5sMC 7xy1C 7xycC 7y1cC 7y22C 7y23C 7y3tC 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_33623.map.gz / Format: CCP4 / Size: 30.5 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: 1.0979 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33623_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33623_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Klebsiella phage Kp7 type I tail fiber
Entire | Name: Klebsiella phage Kp7 type I tail fiber |
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Components |
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-Supramolecule #1: Klebsiella phage Kp7 type I tail fiber
Supramolecule | Name: Klebsiella phage Kp7 type I tail fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Trimer of tail fiber proteins |
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Source (natural) | Organism: Klebsiella phage Kp7 (virus) |
-Macromolecule #1: phage tail fiber
Macromolecule | Name: phage tail fiber / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp7 (virus) |
Molecular weight | Theoretical: 73.019125 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MSVTRLTSSL VRWKSKLANA IQRSLSSKME ESLSVLDFGA VADYNPTTKT GTDNTQAFRN AVAAAIAQNI RNVYAPGGPS AYMTTGEIN LGGEGFTGGE GSRDVWRGIT QGVHFFGDGP YSTIIAFNPP NTDAPCFSAR GGWGTHSPRA LSKLAIEPVN W ADYNATSS ...String: MSVTRLTSSL VRWKSKLANA IQRSLSSKME ESLSVLDFGA VADYNPTTKT GTDNTQAFRN AVAAAIAQNI RNVYAPGGPS AYMTTGEIN LGGEGFTGGE GSRDVWRGIT QGVHFFGDGP YSTIIAFNPP NTDAPCFSAR GGWGTHSPRA LSKLAIEPVN W ADYNATSS GTGVLLQGCC FVPVTDVHIG RFHRGIHFWN KLQGTDDPTN TFTKGDFTEF NRITRVRVFN CDIDVDYQVS LG NNSFHGN SFTDCMCQIN SYGGIGMRMW DDGSRNAIRP SSLPYEYIAN VYNNKHEINW FGSDARTCYL MHIDKAQGRG CNG DMTVEA AVTLRAIGQY WYQSFGSLHS ISAINTVVDG DTDTATRPVA FMWMNSAYPQ VNFDGTDPLL TSGLTPRQYD LNNS GNTGM ELLNIRGANT GAIWSIQNGA ALGWILGRRA QADSRKGTRS VWQFSYNGEV IKSVSAANVG LQNSTGAGFG MLGDT LLRP YAASTISLGS PTYPFTRLRT TDWTVDTNGI VPVQDGIKNI GSSSLRVGTV FAATGTINTS DARLKTEVRP FTSEEI LAA KALSEEIGMY QWVASIESKG DNAREHCGLT VQRAMEVMQQ HGLDPFNYGF ICHDVWDEVV EVSDETGEVI SSTPAGD RY SFRFDQLSLF ISRGIEARMS ELESRM |
-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 R1.2/1.3 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7y5s: |