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- PDB-7e1y: Staphylothermus marinus amylopullulanase -SmApu -

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Basic information

Entry
Database: PDB / ID: 7e1y
TitleStaphylothermus marinus amylopullulanase -SmApu
ComponentsGlycoside hydrolase, family 57
KeywordsHYDROLASE / 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 / carbohydrate metabolic process / hydrolase activity / Glycoside hydrolase, family 57
Function and homology information
Biological speciesStaphylothermus marinus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / negative staining / cryo EM / Resolution: 2.9 Å
AuthorsLi, D. / Li, X. / Woo, E.-J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31671801 China
CitationJournal: To Be Published
Title: Staphylothermus marinus amylopullulanase -SmApu
Authors: Li, D. / Li, X.
History
DepositionFeb 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
A: Glycoside hydrolase, family 57
B: Glycoside hydrolase, family 57
C: Glycoside hydrolase, family 57
D: Glycoside hydrolase, family 57
E: Glycoside hydrolase, family 57
F: Glycoside hydrolase, family 57
G: Glycoside hydrolase, family 57
H: Glycoside hydrolase, family 57


Theoretical massNumber of molelcules
Total (without water)607,8698
Polymers607,8698
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area23990 Å2
ΔGint-110 kcal/mol
Surface area162780 Å2

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Components

#1: Protein
Glycoside hydrolase, family 57


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

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The octamer of glycoside hydrolase family 57. / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Staphylothermus marinus (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: YES / Vitrification applied: YES
EM stainingType: NEGATIVE / Material: Uranyl acetate
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingAverage exposure time: 8 sec. / Electron dose: 64 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 272770 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00436920
ELECTRON MICROSCOPYf_angle_d0.63150200
ELECTRON MICROSCOPYf_dihedral_angle_d13.6664768
ELECTRON MICROSCOPYf_chiral_restr0.0485312
ELECTRON MICROSCOPYf_plane_restr0.0056360

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