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Yorodumi- EMDB-33507: Cryo-EM structure of Klebsiella phage Kp9 type I tail fiber gp42 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33507 | |||||||||
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Title | Cryo-EM structure of Klebsiella phage Kp9 type I tail fiber gp42 in vitro | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Phage type I tail fiber / VIRAL PROTEIN | |||||||||
Biological species | Klebsiella phage Kp9 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 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_33507.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-33507-v30.xml emd-33507.xml | 10.4 KB 10.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33507_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_33507.png | 15.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33507 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33507 | HTTPS FTP |
-Related structure data
Related structure data | 7xy1MC 7xycC 7y1cC 7y22C 7y23C 7y3tC 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_33507.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0742 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Klebsiella phage Kp9 type I tail fiber protein gp42
Entire | Name: Klebsiella phage Kp9 type I tail fiber protein gp42 |
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Components |
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-Supramolecule #1: Klebsiella phage Kp9 type I tail fiber protein gp42
Supramolecule | Name: Klebsiella phage Kp9 type I tail fiber protein gp42 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Trimer of tail fiber proteins |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
-Macromolecule #1: Tail fiber protein
Macromolecule | Name: Tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage Kp9 (virus) |
Molecular weight | Theoretical: 84.120445 KDa |
Recombinant expression | Organism: Escherichia (bacteria) |
Sequence | String: MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ ...String: MDQDIKTVIQ YPVGTTEFDI PFDYLSRKFV RVSLVSDDNR RLLSNITEYR YVSKTRVKLL VATTGFDRVE IRRFTSASER IVDFSDGSV LRANDLNVSQ LQSAHIAEEA RDAALLAMPE DDAGNLDARN RKIVRLAPGE AGTDAINKNQ LDTTLGEAGG I LSEVKDLQ KDMEDYLQNW GDDTTAIRGV LWVYNQGSAV GGETSFVITK EGPVLAVPYI EINGSRQYRG WHYEYDLGSK TI TLAKPLS AGDLVVCTTA ETTLPLADSL AGPTGASQIG TANGLNVQIA LDNLRSGVNV LDFMTFAERA AVLNYTGTND NSE AFRKAF ATGSRQIIVP PGRYHVKDVE IPSKVKLFGT YSYKPYNVTS DASFGTDGTI IRKVAGADNM FLWNTACAAE GVMF DGRDR TSPAIQSKSG GKISVGFFKC GFYRFDRVGN RRGAYIGCSF QFCNFNQNNI GIYNTVDGNH IGCTINANKS HGVML ETGA NSNTFTNCRN EWNEGDNWNF YGATSIQVIN ELCDRAFGYG FRISNSSVTL INVNIRRSAR TAASGAASAQ IYFESS TLK MIGVNSSVGG DDTGGSITEP SPDYFFRMAG TSEGRLEISD SRLTGYTVGL ISGTARPSVI RVINSPGWED TINEGVA RI SGGRPYIGTM PTATGPANVS PAVLGLSCGG VNTYDNDMFD IHLTIRNTNN GGHNGAILTV LLYREGGAAR ATIVRVDS R SNAVGEGDVN STSADPQQVY QVSVEVTSND ASTFNLLVST KSDNSASYRF RAKVKP |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000 |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 124 |
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Output model | PDB-7xy1: |