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- PDB-9grd: Cryo-electron microscopy structure of glucose/xylose isomerase fr... -

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Basic information

Entry
Database: PDB / ID: 9grd
TitleCryo-electron microscopy structure of glucose/xylose isomerase from Streptomyces rubiginosus with cobalt ions in the active site
ComponentsXylose isomerase
KeywordsMETAL BINDING PROTEIN / cobalt / isomerase / sugars / glucose / xylose / metal ion / Cryo-EM
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
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsSlawek, J. / Klonecka, A. / Rawski, M. / Kozak, M.
Funding support Poland, 1items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
C: Xylose isomerase
D: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,60512
Polymers173,1334
Non-polymers4718
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "D"
d_3ens_1chain "A"
d_4ens_1chain "C"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASNASNGLYGLYBB2 - 3882 - 388
d_12COCOCOCOBG401
d_21ASNASNGLYGLYDD2 - 3882 - 388
d_22COCOCOCODK401
d_31ASNASNGLYGLYAA2 - 3882 - 388
d_32COCOCOCOAE401
d_41ASNASNGLYGLYCC2 - 3882 - 388
d_42COCOCOCOCI401

NCS oper:
IDCodeMatrixVector
1given(-0.99999988984651, -0.00042539133949005, -0.00019836627442113), (-0.00042541082872778, 0.99999990468953, 9.82169047822E-5), (0.00019832447489406, 9.8301281124458E-5, -0.99999997550213)215.11187896574, 0.025037198893116, 213.33139539508
2given(0.99999971746825, -0.00073581856300251, 0.0001537350512427), (-0.00073581419882164, -0.99999972888421, -2.8442308246998E-5), (0.00015375593794109, 2.8329179777582E-5, -0.99999998777828)0.040283859600507, 215.1270196003, 213.33963104033
3given(-0.99999997441872, 8.0788661494572E-5, 0.00021127175606889), (-8.081547929285E-5, -0.99999998867886, -0.000126929628609), (0.00021126149920226, -0.0001269466993902, 0.99999996962656)215.00877271616, 215.06282681635, -0.0041426479174191

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Components

#1: Protein
Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / Plasmid details: Hampton Research / References: UniProt: P24300, xylose isomerase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: glucose/xylose isomerase with cobalt ions / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.043 MDa / Experimental value: NO
Source (natural)Organism: Streptomyces rubiginosus (bacteria)
Buffer solutionpH: 7.4 / Details: 50 mM PBS pH 7.4
Buffer componentConc.: 50 mM / Name: Phosphate-buffered saline / Formula: PBS
SpecimenConc.: 1.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
3EPUimage acquisition
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 33650959
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1772170 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 58.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005212472
ELECTRON MICROSCOPYf_angle_d0.807516884
ELECTRON MICROSCOPYf_chiral_restr0.04641740
ELECTRON MICROSCOPYf_plane_restr0.00882300
ELECTRON MICROSCOPYf_dihedral_angle_d5.0991724
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints3.4998812033063E-12
ens_1d_3BBELECTRON MICROSCOPYNCS constraints1.1595545168724E-12
ens_1d_4BBELECTRON MICROSCOPYNCS constraints2.1454147921618E-12

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