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- PDB-9wvc: CryoEM structure of a dNTPase from Vibrio cholerae with GTP -

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Basic information

Entry
Database: PDB / ID: 9wvc
TitleCryoEM structure of a dNTPase from Vibrio cholerae with GTP
ComponentsDeoxyguanosinetriphosphate triphosphohydrolase-like protein 2
KeywordsANTIMICROBIAL PROTEIN / dNTPase / Vibrio cholerae / defense
Function / homology
Function and homology information


dGTPase activity / dGTP catabolic process
Similarity search - Function
dNTP triphosphohydrolase, type 2 / Phosphohydrolase-associated domain / Phosphohydrolase-associated domain / dNTP triphosphohydrolase / : / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsXu, Z.X. / Zhang, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: CryoEM structure of a dNTPase from Vibrio cholerae
Authors: Xu, Z.X. / Zhang, K.
History
DepositionSep 19, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 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

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Assembly

Deposited unit
A: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
B: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
C: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
D: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
E: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
F: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
G: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
H: Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,23332
Polymers367,7878
Non-polymers4,44624
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2


Mass: 45973.367 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Gene: VC_A0308 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KMM3
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: dNTPase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Source (recombinant)Organism: Escherichia coli B (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 defocus max: 2400 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88901 / Symmetry type: POINT
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226312
ELECTRON MICROSCOPYf_angle_d0.43835424
ELECTRON MICROSCOPYf_dihedral_angle_d13.5053680
ELECTRON MICROSCOPYf_chiral_restr0.0333840
ELECTRON MICROSCOPYf_plane_restr0.0034504

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