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- EMDB-42293: Archaeal highly thermostable GH35 family beta-galactosidase from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-42293
TitleArchaeal highly thermostable GH35 family beta-galactosidase from Desulfurococcus amyloliticus
Map data
Sample
  • Complex: Fungal type GH35 family beta-galactosidase from archaeal hyperthermophilicThermoprotei archaeon Desulfurococcus amyloliticus
    • Protein or peptide: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase
KeywordsGlycoside hydrolase / beta-galactosidase / Lactose hydrolysis / Cryo-EM / Hyperthermophilic Archaea / HYDROLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 superfamily / Beta-galactosidase, domain 2 / Beta-galactosidase, domain 2 / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesDesulfurococcus amylolyticus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsPichkur EB / Rychkov GN
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-20146 Russian Federation
CitationJournal: To Be Published
Title: Archaeal highly thermostable GH35 family beta-galactosidase DabetaGal has a unique seven domain protein fold revealed by Cryo-EM and X-ray structural analysis
Authors: Kil Y / Pichkur EB
History
DepositionOct 10, 2023-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42293.png

Downloads & links

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Map

FileDownload / File: emd_42293.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-4.9646688 - 7.451368
Average (Standard dev.)-0.0016370707 (±0.2761281)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42293_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_42293_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42293_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Fungal type GH35 family beta-galactosidase from archaeal hyperthe...

EntireName: Fungal type GH35 family beta-galactosidase from archaeal hyperthermophilicThermoprotei archaeon Desulfurococcus amyloliticus
Components
  • Complex: Fungal type GH35 family beta-galactosidase from archaeal hyperthermophilicThermoprotei archaeon Desulfurococcus amyloliticus
    • Protein or peptide: Beta-galactosidase
    • Protein or peptide: Beta-galactosidase

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Supramolecule #1: Fungal type GH35 family beta-galactosidase from archaeal hyperthe...

SupramoleculeName: Fungal type GH35 family beta-galactosidase from archaeal hyperthermophilicThermoprotei archaeon Desulfurococcus amyloliticus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Desulfurococcus amylolyticus (archaea)

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Macromolecule #1: Beta-galactosidase

MacromoleculeName: Beta-galactosidase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Desulfurococcus amylolyticus (archaea)
Molecular weightTheoretical: 84.576414 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TLLCGEIHYF RVPKHLWRDR LLKLKRAGGN CVSTYIPWNW HDPREKVVNF TDGTSQWHVA SYYSRDLASF LELAGELGLR VIARPGPYI CSEWDSGGHP NWIYTKAMRL RSLDPGYFKH VVEWYNSVLN ILKPYVEREI VIGIQVENEY FWGNEKYIEK L AEIVEEKL ...String:
TLLCGEIHYF RVPKHLWRDR LLKLKRAGGN CVSTYIPWNW HDPREKVVNF TDGTSQWHVA SYYSRDLASF LELAGELGLR VIARPGPYI CSEWDSGGHP NWIYTKAMRL RSLDPGYFKH VVEWYNSVLN ILKPYVEREI VIGIQVENEY FWGNEKYIEK L AEIVEEKL PGVLVFTNED PYLTRIPNTI DLYPSPWDMR QFDDRLRSYL SSQPGLFKMI MELEGGWFKS SRYGYYPTNR LS IPPEWTE ILLKTAVGMG LNNINIYMFH GGSNPGYYTA KYLASSYDFE ACIREWGELS ERYYRVKRVF TFLNGFQELV TSL KPGETV KTASTCSELL QRVGDHGKIA VLRNTGDNLC YQRLINRGEI IPMWTPIRVP PRYAKIVLLD LVVEGTPFKL VYTS GEALL MKRLGDTVVM IIYGDHGEYT ETAVEVEGGV LDVDIQGDVL IRREGERAYL VVNHTHGEHL AIVKSTRGQN LLLIF TCRC RAEKTWIVDE DLVLISNIYY IGDSRIDEGK VVINAELDED SCGRLLVVTS REIEAISLED LDLDLTRLSK YVYATH IPL SMCRSGKNTY HPLEYRLLED PVFHTLTSIN PSSPLLKNGF YENGIYVYRL RLHLDKKQLG DLLDKHLALI GFSDYAV VS INNEYAGSGY HYIEMSADSL REGVNEVTVI LESTGHPNDG LLYVPNGIYG GVYLGRVGEI RLYKWRKTGF EIPYGPGF D LAEFIANPEP VIKALQE

UniProtKB: Beta-galactosidase

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Macromolecule #2: Beta-galactosidase

MacromoleculeName: Beta-galactosidase / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Desulfurococcus amylolyticus (archaea)
Molecular weightTheoretical: 26.123895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ETYSVDSPGL YITEFKVDDL SRHYVLDPGL EFYYNHYYRI LLFVNKVYVG PLIGPIDITR YLKPGVNEVA LLVEWGVVNP VIGVYQYKV DGEWFIQEGL HGLIEEWFRR SPRGETAEPP ILLGDKAGRV IWVNTVIPYE KEPTSSSPVK LEVDFWGCRI L VFVNGEFI ...String:
ETYSVDSPGL YITEFKVDDL SRHYVLDPGL EFYYNHYYRI LLFVNKVYVG PLIGPIDITR YLKPGVNEVA LLVEWGVVNP VIGVYQYKV DGEWFIQEGL HGLIEEWFRR SPRGETAEPP ILLGDKAGRV IWVNTVIPYE KEPTSSSPVK LEVDFWGCRI L VFVNGEFI GRISDDSPER ELYVPETAVR RGLNNITLLA IVTSRSSGIR GLRLKETYVH ERKEIVFKL

UniProtKB: Beta-galactosidase

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 401183
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER / Software - Name: cryoSPARC

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