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Yorodumi- EMDB-36758: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36758 | |||||||||
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Title | CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 3-phenylpropionate/cinnamic acid dioxygenase / BIOSYNTHETIC PROTEIN | |||||||||
Function / homology | Function and homology information 3-phenylpropanoate dioxygenase / 3-phenylpropionate dioxygenase activity / 3-phenylpropionate dioxygenase complex / 3-phenylpropionate catabolic process / 2 iron, 2 sulfur cluster binding / iron ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (strain K12) (bacteria) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.12 Å | |||||||||
Authors | Jiang WX / Cheng XQ / Ma LX / Xing Q | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of 3-phenylpropionate/cinnamic acid dioxygenase HcaE-HcaF complex Authors: Jiang WX / Cheng XQ / Wu M / Ma LX / Xing Q | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36758.map.gz | 490.1 MB | EMDB map data format | |
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Header (meta data) | emd-36758-v30.xml emd-36758.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_36758.png | 32.5 KB | ||
Filedesc metadata | emd-36758.cif.gz | 5.5 KB | ||
Others | emd_36758_half_map_1.map.gz emd_36758_half_map_2.map.gz | 928.2 MB 928.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36758 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36758 | HTTPS FTP |
-Validation report
Summary document | emd_36758_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_36758_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_36758_validation.xml.gz | 22 KB | Display | |
Data in CIF | emd_36758_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36758 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36758 | HTTPS FTP |
-Related structure data
Related structure data | 8k0aMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36758.map.gz / Format: CCP4 / Size: 1000 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: 0.425 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36758_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36758_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homohexamer of inositol phosphate phosphatase SopB
Entire | Name: Homohexamer of inositol phosphate phosphatase SopB |
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Components |
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-Supramolecule #1: Homohexamer of inositol phosphate phosphatase SopB
Supramolecule | Name: Homohexamer of inositol phosphate phosphatase SopB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
-Macromolecule #1: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha
Macromolecule | Name: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: 3-phenylpropanoate dioxygenase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 51.166047 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MTTPSDLNIY QLIDTQNGRV TPRIYTDPDI YQLELERIFG RCWLFLAHES QIPKPGDFFN TYMGEDAVVV VRQKDGSIKA FLNQCRHRA MRVSYADCGN TRAFTCPYHG WSYGINGELI DVPLEPRAYP QGLCKSHWGL NEVPCVESYK GLIFGNWDTS A PGLRDYLG ...String: MTTPSDLNIY QLIDTQNGRV TPRIYTDPDI YQLELERIFG RCWLFLAHES QIPKPGDFFN TYMGEDAVVV VRQKDGSIKA FLNQCRHRA MRVSYADCGN TRAFTCPYHG WSYGINGELI DVPLEPRAYP QGLCKSHWGL NEVPCVESYK GLIFGNWDTS A PGLRDYLG DIAWYLDGML DRREGGTEIV GGVQKWVINC NWKFPAEQFA SDQYHALFSH ASAVQVLGAK DDGSDKRLGD GQ TARPVWE TAKDALQFGQ DGHGSGFFFT EKPDANVWVD GAVSSYYRET YAEAEQRLGE VRALRLAGHN NIFPTLSWLN GTA TLRVWH PRGPDQVEVW AFCITDKAAS DEVKAAFENS ATRAFGPAGF LEQDDSENWC EIQKLLKGHR ARNSKLCLEM GLGQ EKRRD DGIPGITNYI FSETAARGMY QRWADLLSSE SWQEVLDKTA AYQQEVMK UniProtKB: 3-phenylpropionate/cinnamic acid dioxygenase subunit alpha |
-Macromolecule #2: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta
Macromolecule | Name: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: 3-phenylpropanoate dioxygenase |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 20.609248 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MSAQVSLELH HRISQFLFHE ASLLDDWKFR DWLAQLDEEI RYTMRTTVNA QTRDRRKGVQ PPTTWIFNDT KDQLERRIAR LETGMAWAE EPPSRTRHLI SNCQISETDI PNVFAVRVNY LLYRAQKERD ETFYVGTRFD KVRRLEDDNW RLLERDIVLD Q AVITSHNL SVLF UniProtKB: 3-phenylpropionate/cinnamic acid dioxygenase subunit beta |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30478 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |