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- EMDB-51521: Cryo-electron microscopy structure of glucose/xylose isomerase fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-51521
TitleCryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with cobalt ions in the active site
Map dataVolume map
Sample
  • Complex: glucose/xylose isomerase with cobalt ions
    • Protein or peptide: Xylose isomerase
  • Ligand: COBALT (II) ION
  • Ligand: water
Keywordscobalt / isomerase / sugars / glucose / xylose / metal ion / Cryo-EM / METAL BINDING PROTEIN
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
Biological speciesStreptomyces rubiginosus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsSlawek J / Klonecka A / Rawski M / Kozak M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2020/39/O/ST4/03465 Poland
CitationJournal: To Be Published
Title: Cryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with cobalt ions in the active site
Authors: Slawek J / Klonecka A / Kozak M / Rawski M
History
DepositionSep 11, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51521.png

Downloads & links

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Map

FileDownload / File: emd_51521.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVolume map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å		0.84 Å/pix.
x 256 pix.
= 215.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.26979837 - 1.131513
Average (Standard dev.)0.0014118061 (±0.047303613)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 215.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map sharp

Fileemd_51521_additional_1.map
Annotationmap sharp
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_51521_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_51521_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : glucose/xylose isomerase with cobalt ions

EntireName: glucose/xylose isomerase with cobalt ions
Components
  • Complex: glucose/xylose isomerase with cobalt ions
    • Protein or peptide: Xylose isomerase
  • Ligand: COBALT (II) ION
  • Ligand: water

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Supramolecule #1: glucose/xylose isomerase with cobalt ions

SupramoleculeName: glucose/xylose isomerase with cobalt ions / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Streptomyces rubiginosus (bacteria)
Molecular weightTheoretical: 43 KDa

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Macromolecule #1: Xylose isomerase

MacromoleculeName: Xylose isomerase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: xylose isomerase
Source (natural)Organism: Streptomyces rubiginosus (bacteria)
Molecular weightTheoretical: 43.283297 KDa
SequenceString: MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP FGSSDSEREE HVKRFRQALD DTGMKVPMA TTNLFTHPVF KDGGFTANDR DVRRYALRKT IRNIDLAVEL GAETYVAWGG REGAESGGAK DVRDALDRMK E AFDLLGEY ...String:
MNYQPTPEDR FTFGLWTVGW QGRDPFGDAT RRALDPVESV RRLAELGAHG VTFHDDDLIP FGSSDSEREE HVKRFRQALD DTGMKVPMA TTNLFTHPVF KDGGFTANDR DVRRYALRKT IRNIDLAVEL GAETYVAWGG REGAESGGAK DVRDALDRMK E AFDLLGEY VTSQGYDIRF AIEPKPNEPR GDILLPTVGH ALAFIERLER PELYGVNPEV GHEQMAGLNF PHGIAQALWA GK LFHIDLN GQNGIKYDQD LRFGAGDLRA AFWLVDLLES AGYSGPRHFD FKPPRTEDFD GVWASAAGCM RNYLILKERA AAF RADPEV QEALRASRLD ELARPTAADG LQALLDDRSA FEEFDVDAAA ARGMAFERLD QLAMDHLLGA RG

UniProtKB: Xylose isomerase

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Macromolecule #2: COBALT (II) ION

MacromoleculeName: COBALT (II) ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: CO
Molecular weightTheoretical: 58.933 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration1.04 mg/mL
BufferpH: 7.4 / Component - Concentration: 50.0 mM / Component - Formula: PBS / Component - Name: Phosphate-buffered saline / Details: 50 mM PBS pH 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 33650959
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1772170
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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