+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37940 | |||||||||
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Title | Partially closed falcilysin, from free falcilysin dataset | |||||||||
Map data | ||||||||||
Sample |
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Keywords | falcilysin partially closed conformation / HYDROLASE | |||||||||
Function / homology | Function and homology information hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / protein processing / metalloendopeptidase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Lin JQ / Yan XF / Lescar J | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: To Be Published Title: Partially closed falcilysin, from free falcilysin dataset Authors: Lin JQ / Yan XF / Lescar J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37940.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-37940-v30.xml emd-37940.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37940_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_37940.png | 20.4 KB | ||
Masks | emd_37940_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-37940.cif.gz | 5.8 KB | ||
Others | emd_37940_additional_1.map.gz emd_37940_additional_2.map.gz emd_37940_half_map_1.map.gz emd_37940_half_map_2.map.gz | 1.2 MB 7.5 MB 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37940 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37940 | HTTPS FTP |
-Validation report
Summary document | emd_37940_validation.pdf.gz | 853.7 KB | Display | EMDB validaton report |
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Full document | emd_37940_full_validation.pdf.gz | 853.3 KB | Display | |
Data in XML | emd_37940_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_37940_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37940 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37940 | HTTPS FTP |
-Related structure data
Related structure data | 8wyxMC 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_37940.map.gz / Format: CCP4 / Size: 8 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: 1.146 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_37940_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_37940_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_37940_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37940_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37940_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Falcilysin
Entire | Name: Falcilysin |
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Components |
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-Supramolecule #1: Falcilysin
Supramolecule | Name: Falcilysin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
-Macromolecule #1: Falcilysin
Macromolecule | Name: Falcilysin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Plasmodium falciparum 3D7 (eukaryote) |
Molecular weight | Theoretical: 132.220375 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EWIHEKSPKH NSYDIIEKRY NEEFKMTYTV YQHKKAKTQV ISLGTNDPLD VEQAFAFYVK TLTHSGKGIP HILEHSVLSG SKNYNYKNS IGLLEKGTLH THLNAYTFND RTVYMAGSMN NKDFFNIMGV YMDSVFQPNV LENKYIFETE GWTYEVEKLK E DEKGKAEI ...String: EWIHEKSPKH NSYDIIEKRY NEEFKMTYTV YQHKKAKTQV ISLGTNDPLD VEQAFAFYVK TLTHSGKGIP HILEHSVLSG SKNYNYKNS IGLLEKGTLH THLNAYTFND RTVYMAGSMN NKDFFNIMGV YMDSVFQPNV LENKYIFETE GWTYEVEKLK E DEKGKAEI PQMKDYKVSF NGIVYNEMKG ALSSPLEDLY HEEMKYMFPD NVHSNNSGGD PKEITNLTYE EFKEFYYKNY NP KKVKVFF FSKNNPTELL NFVDQYLGQL DYSKYRDDAV ESVEYQTYKK GPFYIKKKYG DHSEEKENLV SVAWLLNPKV DKT NNHNNN HSNNQSSENN GYSNGSHSSD LSLENPTDYF VLLIINNLLI HTPESVLYKA LTDCGLGNNV IDRGLNDSLV QYIF SIGLK GIKRNNEKIK NFDKVHYEVE DVIMNALKKV VKEGFNKSAV EASINNIEFI LKEANLKTSK SIDFVFEMTS KLNYN RDPL LIFEFEKYLN IVKNKIKNEP MYLEKFVEKH FINNAHRSVI LLEGDENYAQ EQENLEKQEL KKRIENFNEQ EKEQVI KNF EELSKYKNAE ESPEHLNKFP IISISDLNKK TLEVPVNVYF TNINENNNIM ETYNKLKTNE HMLKDNMDVF LKKYVLK ND KHNTNNNNNN NNNMDYSFTE TKYEGNVPIL VYEMPTTGIV YLQFVFSLDH LTVDELAYLN LFKTLILENK TNKRSSED F VILREKNIGS MSANVALYSK DDHLNVTDKY NAQALFNLEM HVLSHKCNDA LNIALEAVKE SDFSNKKKVI DILKRKING MKTTFSEKGY AILMKYVKAH LNSKHYAHNI IYGYENYLKL QEQLELAEND FKTLENILVR IRNKIFNKKN LMVSVTSDYG ALKHLFVNS NESLKNLVSY FEENDKYIND MQNKVNDPTV MGWNEEIKSK KLFDEEKVKK EFFVLPTFVN SVSMSGILFK P GEYLDPSF TVIVAALKNS YLWDTVRGLN GAYGVFADIE YDGSVVFLSA RDPNLEKTLA TFRESAKGLR KMADTMTEND LL RYIINTI GTIDKPRRGI ELSKLSFLRL ISNESEQDRV EFRKRIMNTK KEDFYKFADL LESKVNEFEK NIVIITTKEK ANE YIANVD GEFKKVLI UniProtKB: Falcilysin |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-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 / Details: 20 mM Na HEPES, 300 mM NaCl, 0.5 mM TCEP, pH 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |