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- PDB-9slp: CryoEM structure of nucleoside diphosphate kinase (NDK) from Stre... -

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Basic information

Entry
Database: PDB / ID: 9slp
TitleCryoEM structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / kinase / hexamer / soluble protein
Function / homology
Function and homology information


nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsNouri, P. / Giraud, M.-F. / Lambert, O. / Daury, L. / Kaplan, E. / Jault, J.M. / Kerboeuf, J. / Gonzalez, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: CryoEM structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
Authors: Nouri, P. / Giraud, M.-F. / Lambert, O. / Daury, L. / Kaplan, E. / Jault, J.M. / Kerboeuf, J. / Gonzalez, C.
History
DepositionSep 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)105,7746
Polymers105,7746
Non-polymers00
Water00
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
Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 17628.957 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: hexamer , soluble protein kinase, Transferase / Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: ndk, spr1775 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P65537, nucleoside-diphosphate kinase
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: Hexameric form of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
Type: COMPLEX / Details: Apo form / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Streptococcus pneumoniae R6 (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4 / Details: 50 mM Hepes pH 7.4, 100 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHepes1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.69 sec. / Electron dose: 59.5 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3184
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
7PHENIX1.21.2_5419model fitting
9PHENIX1.21.2_5419model refinement
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12cryoSPARC4.6.0classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3231210
SymmetryPoint symmetry: D3 (2x3 fold dihedral)
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 531268 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 2.47 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026654
ELECTRON MICROSCOPYf_angle_d0.4368970
ELECTRON MICROSCOPYf_dihedral_angle_d3.405882
ELECTRON MICROSCOPYf_chiral_restr0.042972
ELECTRON MICROSCOPYf_plane_restr0.0041176

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