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- PDB-9vzi: Cyanopodophage Pan3 Needle -

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Basic information

Entry
Database: PDB / ID: 9vzi
TitleCyanopodophage Pan3 Needle
ComponentsNeedle protein
KeywordsVIRUS / Cyanophage / Needle
Function / homologyIODIDE ION / :
Function and homology information
Biological speciesPseudanabaena phage Pan3 (virus)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.6 Å
AuthorsHou, P. / Zhou, C.Z. / Jiang, Y.L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32430001 China
National Natural Science Foundation of China (NSFC)92451302 China
CitationJournal: To Be Published
Title: Cryo-EM structure of cyanopodophage Pan3 reveals a new host recognition mode
Authors: Hou, P. / Zhou, C.Z. / Jiang, Y.L.
History
DepositionJul 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Needle protein
C: Needle protein
D: Needle protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,81713
Polymers60,7573
Non-polymers1,06010
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-23 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.403, 71.403, 172.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11C-361-

HOH

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Components

#1: Protein Needle protein


Mass: 20252.242 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudanabaena phage Pan3 (virus) / Gene: Pan3_08 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AA49CMD6
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 32.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.0 1.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.6→13.02 Å / Num. obs: 14321 / % possible obs: 99.2 % / Redundancy: 16.5 % / CC1/2: 0.998 / Net I/σ(I): 26.7
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 12 % / Mean I/σ(I) obs: 9.2 / Num. unique obs: 1877 / CC1/2: 0.978 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
REFMAC5refinement
CRANK2phasing
Cootmodel building
CrysalisProdata reduction
CrysalisProdata scaling
Aimlessdata scaling
CrysalisProdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.6→13.02 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2199 656 4.58 %
Rwork0.1809 --
obs0.1828 14319 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→13.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2547 0 40 191 2778
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082607
X-RAY DIFFRACTIONf_angle_d0.9833555
X-RAY DIFFRACTIONf_dihedral_angle_d6.537390
X-RAY DIFFRACTIONf_chiral_restr0.058438
X-RAY DIFFRACTIONf_plane_restr0.007471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.28351280.19032669X-RAY DIFFRACTION100
2.8-3.080.20961200.18372687X-RAY DIFFRACTION100
3.08-3.510.21241340.17162688X-RAY DIFFRACTION100
3.51-4.40.18741200.15952754X-RAY DIFFRACTION100

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