+Open data
-Basic information
Entry | Database: PDB / ID: 7e1y | ||||||
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Title | Staphylothermus marinus amylopullulanase -SmApu | ||||||
Components | Glycoside hydrolase, family 57 | ||||||
Keywords | HYDROLASE / amylopullulanase | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 2.9 Å | ||||||
Authors | Li, D. / Li, X. / Woo, E.-J. | ||||||
Funding support | China, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7e1y.cif.gz | 754.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e1y.ent.gz | 647.4 KB | Display | PDB format |
PDBx/mmJSON format | 7e1y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e1/7e1y ftp://data.pdbj.org/pub/pdb/validation_reports/e1/7e1y | HTTPS FTP |
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-Related structure data
Related structure data | 30946MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 75983.641 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea) Strain: ATCC 43588 / DSM 3639 / JCM 9404 / F1 / Gene: Smar_1407 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A3DPD7 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: The octamer of glycoside hydrolase family 57. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Staphylothermus marinus (archaea) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES |
EM staining | Type: NEGATIVE / Material: Uranyl acetate |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm |
Image recording | Average exposure time: 8 sec. / Electron dose: 64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272770 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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