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Yorodumi- EMDB-32219: Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32219 | ||||||||||||
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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 / HYDROLASE | ||||||||||||
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: 2.46 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_32219.map.gz | 59.1 MB | EMDB map data format | |
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Header (meta data) | emd-32219-v30.xml emd-32219.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_32219_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_32219.png | 18.9 KB | ||
Others | emd_32219_additional_1.map.gz emd_32219_half_map_1.map.gz emd_32219_half_map_2.map.gz | 59 MB 49.8 MB 49.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32219 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32219 | HTTPS FTP |
-Related structure data
Related structure data | 7vz3MC 7vyvC 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_32219.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_32219_additional_1.map | ||||||||||||
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Annotation | sharpened by b-factor -50 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_32219_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32219_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: 100.947852 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MMALYREGKA AMAADGTVTG TGTKWQSSLS LIRPGATIMF LSSPIQMAVV NKVVSDTEIK AITTNGAVV ASTDYAILLS DSLTVDGLAQ DVAETLRYYQ SQETVIADAV EFFKEFDFES LQNLANQIKA DSEASESSAA A AAASESKA ...String: MGSSHHHHHH SSGLVPRGSH MMALYREGKA AMAADGTVTG TGTKWQSSLS LIRPGATIMF LSSPIQMAVV NKVVSDTEIK AITTNGAVV ASTDYAILLS DSLTVDGLAQ DVAETLRYYQ SQETVIADAV EFFKEFDFES LQNLANQIKA DSEASESSAA A AAASESKA KTSEDNAKSS ENAAKNSEVA AETTRDQIQQ IIDNAGDQST LVVLAQPDGF DSIGRVSSFA ALRNLKPKKS GQ HVLLTSY YDGWAAENKM PTGGGEFISS IGTATDDGGY IAAGPGYYWT RVVNNNSFTA EDFGCKTTAT PPPNFNVLPA ELF DNTARM QAAFNLAISK SFKLNLSAGT YYFESSDTLR ITGPIHIEGR PGTVFYHNPS NKANPKTDAF MNISGCSMGR ISSI NCFSN SYLGKGINFD RSVGDNRKLV LEHVYVDTFR WGFYVGEPEC INQIEFHSCR AQSNYFQGIF IESFKEGQEY GHSAP VHFF NTICNGNGPT SFALGATYKT TKNEYIKVMD SVNDVGCQAY FQGLSNVQYI GGQLSGHGSP RNTSLATITQ CNSFII YGT DLEDINGFTT DGTAITADNI DTIESNYLKD ISGAAIVVSS CLGFKIDSPH IFKIKTLSTI KLMNNTYNYE IGGFTPD EA LKYNVWDANG LATNRISGVI HPRLVNSRLG INSVAFDNMS NKLDVSSLIH NETSQIIGLT PSTGSNVPHT RIMWSNGA M YSSTDLNNGF RLNYLSNHNE PLTPMHLYNE FSVSEFGGSV TESNALDEIK YIFIQTTYAN SGDGRFIIQA LDASGSVLS SNWYSPQSFN STFPISGFVR FDVPTGAKKI RYGFVNSANY TGSLRSHFMS GFAYNKRFFL KIYAVYNDLG RYGQFEPPYS VAIDRFRVG DNTTQMPSIP ASSATDVAGV NEVINSLLAS LKANGFMSS 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 or 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-7vz3: |