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- EMDB-30946: Staphylothermus marinus amylopullulanase -SmApu -

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Basic information

Entry
Database: EMDB / ID: EMD-30946
TitleStaphylothermus marinus amylopullulanase -SmApu
Map data
Sample
  • Complex: The octamer of glycoside hydrolase family 57.
    • Protein or peptide: Glycoside hydrolase, family 57
Keywordsamylopullulanase / HYDROLASE
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) / Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 2.9 Å
AuthorsLi D / Li X
Funding support China, 1 items
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, 2021-
Header (metadata) releaseFeb 9, 2022-
Map releaseFeb 9, 2022-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7e1y
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7e1y
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30946.png

Downloads & links

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Map

FileDownload / File: emd_30946.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å		1.01 Å/pix.
x 300 pix.
= 304.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.014 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.025
Minimum - Maximum-0.08265567 - 0.16648026
Average (Standard dev.)0.0002937544 (±0.004722529)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 304.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0141.0141.014
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z304.200304.200304.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0830.1660.000

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Supplemental data

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Mask #1

Fileemd_30946_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30946_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_30946_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The octamer of glycoside hydrolase family 57.

EntireName: The octamer of glycoside hydrolase family 57.
Components
  • Complex: The octamer of glycoside hydrolase family 57.
    • Protein or peptide: Glycoside hydrolase, family 57

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Supramolecule #1: The octamer of glycoside hydrolase family 57.

SupramoleculeName: The octamer of glycoside hydrolase family 57. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Staphylothermus marinus (archaea)

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Macromolecule #1: Glycoside hydrolase, family 57

MacromoleculeName: Glycoside hydrolase, family 57 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Staphylothermus marinus (strain ATCC 43588 / DSM 3639 / JCM 9404 / F1) (archaea)
Strain: ATCC 43588 / DSM 3639 / JCM 9404 / F1
Molecular weightTheoretical: 75.983641 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

UniProtKB: Glycoside hydrolase, family 57

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 7.5
StainingType: NEGATIVE / Material: Uranyl acetate
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Ab initio model from Relion
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272770
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7e1y:
Staphylothermus marinus amylopullulanase -SmApu

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