+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37941 | |||||||||
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Title | Open falcilysin, from free falcilysin dataset | |||||||||
Map data | ||||||||||
Sample |
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Keywords | falcilysin open conformation / HYDROLASE | |||||||||
Function / homology | Function and homology information hemoglobin catabolic process / apicoplast / food vacuole / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / vacuolar membrane / metalloendopeptidase activity / protein processing / metal ion binding Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum 3D7 (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Lin JQ / Yan XF / Lescar J | |||||||||
Funding support | Singapore, 1 items
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Citation | Journal: To Be Published Title: Open 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_37941.map.gz | 6 MB | EMDB map data format | |
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Header (meta data) | emd-37941-v30.xml emd-37941.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37941_fsc.xml | 4.6 KB | Display | FSC data file |
Images | emd_37941.png | 20 KB | ||
Masks | emd_37941_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-37941.cif.gz | 5.9 KB | ||
Others | emd_37941_additional_1.map.gz emd_37941_additional_2.map.gz emd_37941_half_map_1.map.gz emd_37941_half_map_2.map.gz | 7.5 MB 1.3 MB 6 MB 6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37941 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37941 | HTTPS FTP |
-Validation report
Summary document | emd_37941_validation.pdf.gz | 860 KB | Display | EMDB validaton report |
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Full document | emd_37941_full_validation.pdf.gz | 859.5 KB | Display | |
Data in XML | emd_37941_validation.xml.gz | 10.1 KB | Display | |
Data in CIF | emd_37941_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37941 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37941 | HTTPS FTP |
-Related structure data
Related structure data | 8wyyMC 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_37941.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_37941_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_37941_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_37941_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37941_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37941_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: 132.034156 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: IHEKSPKHNS YDIIEKRYNE EFKMTYTVYQ HKKAKTQVIS LGTNDPLDVE QAFAFYVKTL THSGKGIPHI LEHSVLSGSK NYNYKNSIG LLEKGTLHTH LNAYTFNDRT VYMAGSMNNK DFFNIMGVYM DSVFQPNVLE NKYIFETEGW TYEVEKLKED E KGKAEIPQ ...String: IHEKSPKHNS YDIIEKRYNE EFKMTYTVYQ HKKAKTQVIS LGTNDPLDVE QAFAFYVKTL THSGKGIPHI LEHSVLSGSK NYNYKNSIG LLEKGTLHTH LNAYTFNDRT VYMAGSMNNK DFFNIMGVYM DSVFQPNVLE NKYIFETEGW TYEVEKLKED E KGKAEIPQ MKDYKVSFNG IVYNEMKGAL SSPLEDLYHE EMKYMFPDNV HSNNSGGDPK EITNLTYEEF KEFYYKNYNP KK VKVFFFS KNNPTELLNF VDQYLGQLDY SKYRDDAVES VEYQTYKKGP FYIKKKYGDH SEEKENLVSV AWLLNPKVDK TNN HNNNHS NNQSSENNGY SNGSHSSDLS LENPTDYFVL LIINNLLIHT PESVLYKALT DCGLGNNVID RGLNDSLVQY IFSI GLKGI KRNNEKIKNF DKVHYEVEDV IMNALKKVVK EGFNKSAVEA SINNIEFILK EANLKTSKSI DFVFEMTSKL NYNRD PLLI FEFEKYLNIV KNKIKNEPMY LEKFVEKHFI NNAHRSVILL EGDENYAQEQ ENLEKQELKK RIENFNEQEK EQVIKN FEE LSKYKNAEES PEHLNKFPII SISDLNKKTL EVPVNVYFTN INENNNIMET YNKLKTNEHM LKDNMDVFLK KYVLKND KH NTNNNNNNNN NMDYSFTETK YEGNVPILVY EMPTTGIVYL QFVFSLDHLT VDELAYLNLF KTLILENKTN KRSSEDFV I LREKNIGSMS ANVALYSKDD HLNVTDKYNA QALFNLEMHV LSHKCNDALN IALEAVKESD FSNKKKVIDI LKRKINGMK TTFSEKGYAI LMKYVKAHLN SKHYAHNIIY GYENYLKLQE QLELAENDFK TLENILVRIR NKIFNKKNLM VSVTSDYGAL KHLFVNSNE SLKNLVSYFE ENDKYINDMQ NKVNDPTVMG WNEEIKSKKL FDEEKVKKEF FVLPTFVNSV SMSGILFKPG E YLDPSFTV IVAALKNSYL WDTVRGLNGA YGVFADIEYD GSVVFLSARD PNLEKTLATF RESAKGLRKM ADTMTENDLL RY IINTIGT IDKPRRGIEL SKLSFLRLIS NESEQDRVEF RKRIMNTKKE DFYKFADLLE SKVNEFEKNI VIITTKEKAN EYI ANVDGE FKKVLIE 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 |