+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30946 | |||||||||
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Title | Staphylothermus marinus amylopullulanase -SmApu | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Glycoside hydrolase family 57, N-terminal domain / Glycosyl hydrolase family 57 / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / hydrolase activity / carbohydrate metabolic process / Glycoside hydrolase, family 57 Function and homology information | |||||||||
Biological species | Staphylothermus marinus (archaea) / Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 2.9 Å | |||||||||
Authors | Li D / Li X / Woo E-J | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Staphylothermus marinus amylopullulanase -SmApu Authors: Li D / Li X | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_30946.map.gz | 10.9 MB | EMDB map data format | |
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Header (meta data) | emd-30946-v30.xml emd-30946.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30946_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_30946.png | 90 KB | ||
Masks | emd_30946_msk_1.map | 103 MB | Mask map | |
Others | emd_30946_half_map_1.map.gz emd_30946_half_map_2.map.gz | 80.9 MB 80.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30946 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30946 | HTTPS FTP |
-Related structure data
Related structure data | 7e1yMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_30946.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_30946_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_30946_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_30946_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The octamer of glycoside hydrolase family 57.
Entire | Name: The octamer of glycoside hydrolase family 57. |
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Components |
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-Supramolecule #1: The octamer of glycoside hydrolase family 57.
Supramolecule | Name: The octamer of glycoside hydrolase family 57. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Staphylothermus marinus (archaea) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Glycoside hydrolase, family 57
Macromolecule | Name: Glycoside hydrolase, family 57 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea) Strain: ATCC 43588 / DSM 3639 / JCM 9404 / F1 |
Molecular weight | Theoretical: 75.983641 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: LEVLDKYSSL IKPKLINNIE AYMVFDKPAH KPNAEAKIYV LLNNHGSRRD IHYKIVSIDR NREVFSKRIN VDEKKFLIET ISIETPDKP GRFCYKLFID NEQIDNTCFL VGDPSSREQM YFTIVWHHHQ APNYLPDGRI HGPWAYIYVW SDLLKPYGKG P YHYHSVML ...String: LEVLDKYSSL IKPKLINNIE AYMVFDKPAH KPNAEAKIYV LLNNHGSRRD IHYKIVSIDR NREVFSKRIN VDEKKFLIET ISIETPDKP GRFCYKLFID NEQIDNTCFL VGDPSSREQM YFTIVWHHHQ APNYLPDGRI HGPWAYIYVW SDLLKPYGKG P YHYHSVML NIHPHFKATY NLSPSLLRQW QIAVEKGVEF VNGEKYDPNH EKIRLVEETL NNYREALFKG QIDVLTSIYA HT IGGFLTD VLGATNIVEE EIRYGKEVTS KIMGNNYNPQ GIWTPEMAFS MKLIPIYYDL DIKYTVLDDK FHFFHAEGNK DSQ YEPYMV IDTESKKYIT VFFRDHDLSD ILGFRNNFYS EPHAWRNAYE FALRVAEKWF DKNVKVLTIA LDGENWMSFS VNPP LTAYF LDKMIIYLET LSDNKFIKLS TLREIYNKVP ANRILTNIPT NSWLGTFRKW RGEVPQHEEY WIKTYSVYRK LLAYE EMIG GRDEFSNEAR WALWHALDSD YWWAEFWLPK IIDTWLSVAE NILNNRINKI QIIDVRPASE FYEDEKAGLV VTIRNQ LEK EIRVSFAIGG TGFSSVNNDL ETVKMNPNSS YTRIIPVKAK FIGKHKMVVS AISKGLIIDS KIIDINVKPK LLPNPRL EH HHHHH |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL |
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Buffer | pH: 7.5 |
Staining | Type: NEGATIVE / Material: Uranyl acetate |
Grid | Material: COPPER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 8.0 sec. / Average electron dose: 64.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-7e1y: |