9WX4 | pdb_00009wx4

CryoEM structure of a dNTPase from Vibrio cholerae in hexadecamericmform

PDB DOI: https://doi.org/10.2210/pdb9WX4/pdb
EM Map EMD-66325: EMDB EMDataResource

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-24 Released: 2026-10-07
Deposition Author(s): Xu, Z.X., Zhang, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9WX4

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of a dNTPase from Vibrio cholerae in hexadecamericmform

Xu, Z.X., Zhang, K.

To be published.

Macromolecule Content

Total Structure Weight: 736.63 kDa
Atom Count: 50,044
Modeled Residue Count: 6,208
Deposited Residue Count: 6,432
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyguanosinetriphosphate triphosphohydrolase-like protein 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	402	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 0 Gene Names: VC_A0308
UniProt
Find proteins for Q9KMM3 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KMM3 Go to UniProtKB: Q9KMM3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KMM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain V [auth C] SDF format, chain T [auth B] SDF format, chain RA [auth P] SDF format, chain R [auth A] SDF format, chain PA [auth O] SDF format, chain NA [auth N] SDF format, chain LA [auth M] SDF format, chain IA [auth L] SDF format, chain GA [auth K] MOL2 format, chain DA [auth I] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain V [auth C] MOL2 format, chain T [auth B] MOL2 format, chain RA [auth P] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth O] MOL2 format, chain NA [auth N] MOL2 format, chain LA [auth M] MOL2 format, chain IA [auth L] MOL2 format, chain GA [auth K] mmCIF format, chain DA [auth I] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain V [auth C] mmCIF format, chain T [auth B] mmCIF format, chain RA [auth P] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth O] mmCIF format, chain NA [auth N] mmCIF format, chain LA [auth M] mmCIF format, chain IA [auth L] mmCIF format, chain GA [auth K]	DA [auth I] GA [auth K] IA [auth L] LA [auth M] NA [auth N] DA [auth I], GA [auth K], IA [auth L], LA [auth M], NA [auth N], PA [auth O], R [auth A], RA [auth P], T [auth B], V [auth C], X [auth D], Z [auth E]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain DA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain LA [auth M] Focus chain NA [auth N] Focus chain PA [auth O] Focus chain R [auth A] Focus chain RA [auth P] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth I] Focus chain GA [auth K] Focus chain IA [auth L] Focus chain LA [auth M] Focus chain NA [auth N] Focus chain PA [auth O] Focus chain R [auth A] Focus chain RA [auth P] Focus chain T [auth B] Focus chain V [auth C] Focus chain X [auth D] Focus chain Z [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth H] SDF format, chain KA [auth M] SDF format, chain Q [auth A] SDF format, chain U [auth C] SDF format, chain Y [auth E] SDF format, chain W [auth D] SDF format, chain S [auth B] SDF format, chain QA [auth P] SDF format, chain OA [auth O] SDF format, chain MA [auth N] SDF format, chain JA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain BA [auth G] SDF format, chain AA [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain KA [auth M] MOL2 format, chain Q [auth A] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth E] MOL2 format, chain W [auth D] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth P] MOL2 format, chain OA [auth O] MOL2 format, chain MA [auth N] MOL2 format, chain JA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain BA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain CA [auth H] mmCIF format, chain KA [auth M] mmCIF format, chain Q [auth A] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth E] mmCIF format, chain W [auth D] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth P] mmCIF format, chain OA [auth O] mmCIF format, chain MA [auth N] mmCIF format, chain JA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain BA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth G] CA [auth H] EA [auth I] FA [auth J] AA [auth F], BA [auth G], CA [auth H], EA [auth I], FA [auth J], HA [auth K], JA [auth L], KA [auth M], MA [auth N], OA [auth O], Q [auth A], QA [auth P], S [auth B], U [auth C], W [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain MA [auth N] Focus chain OA [auth O] Focus chain Q [auth A] Focus chain QA [auth P] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain KA [auth M] Focus chain MA [auth N] Focus chain OA [auth O] Focus chain Q [auth A] Focus chain QA [auth P] Focus chain S [auth B] Focus chain U [auth C] Focus chain W [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2026-10-07
Type: Initial release