9VZI | pdb_00009vzi

Cyanopodophage Pan3 Needle

PDB DOI: https://doi.org/10.2210/pdb9VZI/pdb

Classification: VIRUS
Organism(s): Pseudanabaena phage Pan3
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-22 Released: 2025-11-26
Deposition Author(s): Hou, P., Zhou, C.Z., Jiang, Y.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.181 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Cryo-EM structure of cyanopodophage Pan3 reveals a new host recognition mode

Hou, P., Zhou, C.Z., Jiang, Y.L.

To be published.

Macromolecule Content

Total Structure Weight: 61.82 kDa
Atom Count: 2,778
Modeled Residue Count: 357
Deposited Residue Count: 591
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Needle protein	A [auth B], B [auth C], C [auth D]	197	Pseudanabaena phage Pan3	Mutation(s): 0 Gene Names: Pan3_08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain D [auth B] MOL2 format, chain M [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain D [auth B] mmCIF format, chain M [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain D [auth B]	D [auth B], G [auth C], H [auth C], M [auth D]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain M [auth D] Interactions & Density Focus chain D [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain M [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain F [auth B] SDF format, chain E [auth B] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B]	E [auth B] F [auth B] I [auth C] J [auth C] K [auth C] E [auth B], F [auth B], I [auth C], J [auth C], K [auth C], L [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.181 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.403	α = 90
b = 71.403	β = 90
c = 172.706	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
CRANK2	phasing
Coot	model building
CrysalisPro	data reduction
CrysalisPro	data scaling
Aimless	data scaling
CrysalisPro	data collection