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Yorodumi- EMDB-32215: Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32215 | ||||||||||||
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Title | Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targets the K2 serotype K. pneumoniae | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | Depolymerase / Klebsiella pneumoniae / K2 capsular type / Capsular polysaccharides / LYASE | ||||||||||||
Function / homology | biological process involved in interaction with host / Pectin lyase fold/virulence factor / viral life cycle / virion component / Depolymerase Function and homology information | ||||||||||||
Biological species | Klebsiella phage 020009 (virus) / Klebsiella phage GH-K3 (virus) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.32 Å | ||||||||||||
Authors | Cai R / Ren Z | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Depo32, a depolymerase of Klebsiella phage, efficiently controls infection caused by Klebsiella pneumoniae with K2 serotype CPS Authors: Cai R / Ren Z / Zhao R / Wang X / Guo Z / Du R / Han W / Ru H / Gu J | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32215.map.gz | 56.8 MB | EMDB map data format | |
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Header (meta data) | emd-32215-v30.xml emd-32215.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32215_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_32215.png | 115 KB | ||
Others | emd_32215_additional_1.map.gz emd_32215_half_map_1.map.gz emd_32215_half_map_2.map.gz | 56.8 MB 49.7 MB 49.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32215 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32215 | HTTPS FTP |
-Related structure data
Related structure data | 7vyvMC 7vz3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32215.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: sharpened by B-factor -50
File | emd_32215_additional_1.map | ||||||||||||
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Annotation | sharpened by B-factor -50 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32215_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32215_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Tail spike protein Depo32
Entire | Name: Tail spike protein Depo32 |
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Components |
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-Supramolecule #1: Tail spike protein Depo32
Supramolecule | Name: Tail spike protein Depo32 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Klebsiella phage 020009 (virus) / Strain: vB_KpnS_GH-K3 |
Molecular weight | Theoretical: 300 KDa |
-Macromolecule #1: Depolymerase
Macromolecule | Name: Depolymerase / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Klebsiella phage GH-K3 (virus) |
Molecular weight | Theoretical: 98.645289 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MALYREGKAA MAADGTVTGT GTKWQSSLSL IRPGATIMFL SSPIQMAVVN KVVSDTEIKA ITTNGAVVAS TDYAILLSDS LTVDGLAQD VAETLRYYQS QETVIADAVE FFKEFDFESL QNLANQIKAD SEASESSAAA AAASESKAKT SEDNAKSSEN A AKNSEVAA ...String: MALYREGKAA MAADGTVTGT GTKWQSSLSL IRPGATIMFL SSPIQMAVVN KVVSDTEIKA ITTNGAVVAS TDYAILLSDS LTVDGLAQD VAETLRYYQS QETVIADAVE FFKEFDFESL QNLANQIKAD SEASESSAAA AAASESKAKT SEDNAKSSEN A AKNSEVAA ETTRDQIQQI IDNAGDQSTL VVLAQPDGFD SIGRVSSFAA LRNLKPKKSG QHVLLTSYYD GWAAENKMPT GG GEFISSI GTATDDGGYI AAGPGYYWTR VVNNNSFTAE DFGCKTTATP PPNFNVLPAE LFDNTARMQA AFNLAISKSF KLN LSAGTY YFESSDTLRI TGPIHIEGRP GTVFYHNPSN KANPKTDAFM NISGCSMGRI SSINCFSNSY LGKGINFDRS VGDN RKLVL EHVYVDTFRW GFYVGEPECI NQIEFHSCRA QSNYFQGIFI ESFKEGQEYG HSAPVHFFNT ICNGNGPTSF ALGAT YKTT KNEYIKVMDS VNDVGCQAYF QGLSNVQYIG GQLSGHGSPR NTSLATITQC NSFIIYGTDL EDINGFTTDG TAITAD NID TIESNYLKDI SGAAIVVSSC LGFKIDSPHI FKIKTLSTIK LMNNTYNYEI GGFTPDEALK YNVWDANGLA TNRISGV IH PRLVNSRLGI NSVAFDNMSN KLDVSSLIHN ETSQIIGLTP STGSNVPHTR IMWSNGAMYS STDLNNGFRL NYLSNHNE P LTPMHLYNEF SVSEFGGSVT ESNALDEIKY IFIQTTYANS GDGRFIIQAL DASGSVLSSN WYSPQSFNST FPISGFVRF DVPTGAKKIR YGFVNSANYT GSLRSHFMSG FAYNKRFFLK IYAVYNDLGR YGQFEPPYSV AIDRFRVGDN TTQMPSIPAS SATDVAGVN EVINSLLASL KANGFMSS UniProtKB: Depolymerase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285.15 K / Instrument: FEI VITROBOT MARK IV / Details: blot 3.5 to 4 seconds before plunging. | ||||||||||||
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.56 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: RECIPROCAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7vyv: |