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- PDB-9vf5: Cryo-EM structure of apo form of Arthrobacter psychrolactophillus... -

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Basic information

Entry
Database: PDB / ID: 9vf5
TitleCryo-EM structure of apo form of Arthrobacter psychrolactophillus L-arabinose isomerase
ComponentsL-arabinose isomerase
KeywordsSTRUCTURAL PROTEIN / Isomerase / Apo form / enzyme / Arthrobacter psychrolactophilus
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / : / manganese ion binding / cytosol
Similarity search - Function
: / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily
Similarity search - Domain/homology
L-arabinose isomerase
Similarity search - Component
Biological speciesArthrobacter psychrolactophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.52 Å
AuthorsLaksmi, F.A. / Nugraha, Y. / Jayawardena, N. / Raschdorf, O. / Chek, M.F. / Kohga, H. / Herliana, L. / Fathoni, A. / Hidayat, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of apo form of Arthrobacter psychrolactophillus L-arabinose isomerase
Authors: Laksmi, F.A. / Nugraha, Y. / Jayawardena, N. / Raschdorf, O. / Chek, M.F. / Kohga, H. / Herliana, L. / Fathoni, A. / Hidayat, I.
History
DepositionJun 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)334,74612
Polymers334,0136
Non-polymers7336
Water21,4201189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
L-arabinose isomerase


Mass: 55668.887 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter psychrolactophilus (bacteria)
Gene: araA, CVS30_15140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2V5JDW0, L-arabinose isomerase
#2: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: Homo 6-mer of L-arabinose isomerase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.348 MDa / Experimental value: YES
Source (natural)Organism: Arthrobacter psychrolactophilus (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 50 mM Tris-HCl buffer (pH 8.0)
SpecimenConc.: 10 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 R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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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: 215000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21_5207model refinement
3EPU3.12image acquisition
5cryoSPARC4.6.2CTF correction
10cryoSPARC4.6.2initial Euler assignment
13cryoSPARC4.6.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 1.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1732769 / Symmetry type: POINT
RefinementHighest resolution: 1.52 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223886
ELECTRON MICROSCOPYf_angle_d0.50832448
ELECTRON MICROSCOPYf_dihedral_angle_d5.4133293
ELECTRON MICROSCOPYf_chiral_restr0.0423618
ELECTRON MICROSCOPYf_plane_restr0.0044248

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