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Yorodumi- EMDB-33519: CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33519 | |||||||||
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Title | CryoEM structure of Klebsiella phage Kp7 type II tail fiber gp52 in vitro | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Phage type II tail fiber / VIRAL PROTEIN | |||||||||
Biological species | Klebsiella phage Kp7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 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_33519.map.gz | 2.8 MB | EMDB map data format | |
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Header (meta data) | emd-33519-v30.xml emd-33519.xml | 10 KB 10 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33519_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_33519.png | 37.2 KB | ||
Filedesc metadata | emd-33519.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33519 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33519 | HTTPS FTP |
-Validation report
Summary document | emd_33519_validation.pdf.gz | 393.6 KB | Display | EMDB validaton report |
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Full document | emd_33519_full_validation.pdf.gz | 393.1 KB | Display | |
Data in XML | emd_33519_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | emd_33519_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33519 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33519 | HTTPS FTP |
-Related structure data
Related structure data | 7xycMC 7xy1C 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_33519.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: 1.17 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Klebsiella phage Kp7 type II tail fiber
Entire | Name: Klebsiella phage Kp7 type II tail fiber |
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Components |
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-Supramolecule #1: Klebsiella phage Kp7 type II tail fiber
Supramolecule | Name: Klebsiella phage Kp7 type II 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: 61.21027 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MALVKATFVK DVDGQPWRFS SVAKMKAFNY SCYLGSSVFL ESWHEGAGLG SGLFKVSKGT TEVGDDGSVI VAADGTRLIR VFDGPIFAD MWGALPSSTY NSLPAIKSAY LYASSKLQQL FLGGGSYKVT GSSGIDIDPS LAGISALSRA RVDTTEFTGD Y LFTITSSY ...String: MALVKATFVK DVDGQPWRFS SVAKMKAFNY SCYLGSSVFL ESWHEGAGLG SGLFKVSKGT TEVGDDGSVI VAADGTRLIR VFDGPIFAD MWGALPSSTY NSLPAIKSAY LYASSKLQQL FLGGGSYKVT GSSGIDIDPS LAGISALSRA RVDTTEFTGD Y LFTITSSY SYTPAPYYNN LSVALEGLYV FGNKTEGRSG LLTGRRTTDG VKSYNGQTEI RNCTFDKFDY NIRMGHNSWR IV FYKVNSL NALNANGILY VPSGLDDSGE ILTFYHCQFF DGAGSNIRIS CSSFAMTFVS CSFLNITFTI DAGSSVSVTA LGC NFENPG SQSTRRYIEI TAGHTNIFNV VGGSIVTNAN AGQTQALIHV SANNQINLSN LTIPYGAHYQ QEADSGYHAF CSGQ GYVST SNCSLQLLNG AGCCPIHPSL SVFTNWNLSY ANLNAWTVDK GSAPTSVAEY LSAQGPKGEG VLHVAPTTQG VNISQ VATV SKQAGSMSMS VMVNIISASS NAGQISLAYL DAFDNNLGGV SANLGTTTGW KVIGKNTLRG RLPVGTAKVR LNIQTV AGA DVQYTNILCN II |
-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 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: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 36000 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 146 |
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Output model | PDB-7xyc: |