SAXSdb — 3j0i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ029

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 96–390 Chain B； UniProt 96–390 Chain C； UniProt 96–390 Chain D； UniProt 96–390 Chain E； UniProt 96–390 Chain F； UniProt 96–390	Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)	No other associated polymer	ELECTRON MICROSCOPY cryo-EM vitrification conditions：Cryogen ETHANE；liquid ethane	Resolution 19.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3J0I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3J0H Fitting of the bacteriophage phiKZ gp29PR structure into the cryo-EM density map of the phiKZ extended tail sheath Deposited 2011-08-16	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain B 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain C 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain D 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain E 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390) Chain F 96–390（295 aa） Fragment：protease-resistant fragment of gene product 29 (GP29PR, UNP residues 96-390)	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE；liquid ethane	Resolution 18.00 Å
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
3SPE Crystal structure of the tail sheath protein protease resistant fragment from bacteriophage phiKZ Deposited 2011-07-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390) Chain B 96–390（295 aa） Fragment：Protease Resistant Fragment of Gene Product 29 (GP29PR) (UNP residues 96-390)	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M Na/K Phosphate, pH 5.0 with 0.1 M Na Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.286
9XPF The structure of sheath and tube proteins of phage Phikz Deposited 2025-11-16	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric	Chain A 1–695（695 aa） Chain B 1–695（695 aa） Chain C 1–695（695 aa） Chain D 1–695（695 aa） Chain E 1–695（695 aa） Chain F 1–695（695 aa） Chain M 1–695（695 aa） Chain N 1–695（695 aa） Chain O 1–695（695 aa） Chain P 1–695（695 aa） Chain Q 1–695（695 aa） Chain R 1–695（695 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9XPS The neck structure of the Phage Phikz Deposited 2025-11-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric	Chain x 1–695（695 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.52 Å
9XQS Structure of the inner peripheral region in the phage phiKZ baseplate complex Deposited 2025-11-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 84 PDB declaration: 84-meric	Chain W 1–695（695 aa） Chain X 1–695（695 aa） Chain Y 1–695（695 aa） Chain Z 1–695（695 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q8SDD3_BPDPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 96–390 Author chain B； PDBConstruct 1–295； UniProt 96–390 Author chain C； PDBConstruct 1–295； UniProt 96–390 Author chain D； PDBConstruct 1–295； UniProt 96–390 Author chain E； PDBConstruct 1–295； UniProt 96–390 Author chain F； PDBConstruct 1–295； UniProt 96–390

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3j0i
Deposition date deposition_date	2011-08-16
Structure title title	Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath
Keywords keywords	bacteriophage tail sheath, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	— Å
Radius of gyration Rg (electron density) rg_electron	139.00 Å
Forward intensity I(0) i0	360289000.00
Molecular weight molecular_weight	165010.0 kDa
Excluded volume excluded_volume	207050 Å³
Envelope volume envelope_volume	668500 Å³
Hydration-shell volume shell_volume	41178 Å³
Envelope diameter envelope_diameter	325.0 Å
Shell Rg shell_rg	150.70 Å
Envelope Rg envelope_rg	116.10 Å
Shape Rg shape_rg	139.00 Å
Total Rg total_rg	139.20 Å
Total atoms total_atoms	11646
Residues n_residues	1512
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	718.8 Å
Rg (real space) rg_real	133.70 Å
Rg uncertainty (real space) rg_real_error	22.39 Å
I(0) (real space) i0_real	3.5980e+08
I(0) uncertainty (real space) i0_real_error	1.0490e+07
Rg (reciprocal space) rg_reciprocal	128.20 Å
I(0) (reciprocal space) i0_reciprocal	336200000.0000
Solution quality estimate total_estimate	0.6189
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	196.0 Å
Skewness Skewness skewness	-5.671
Kurtosis Kurtosis kurtosis	-42.583
Angular range angular_range	— – 0.0550 Å⁻¹
Current regularization parameter α current_alpha	0.1539
Highest regularization parameter α highest_alpha	100300000.0000
Real-space data points n_real_points	12
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 16.320; Oscil: 0.000; Stabil: 0.887; Sysdev: 1.000; Positv: 1.000; Valcen: 0.396; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	19.00 Å
Resolution测定方法 resolution_method	spider single particle
颗粒数 num_particles	—

Description description	PHIKZ029
Molecular weight formula_weight	32296.9 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11646

Fitting of the phiKZ gp29PR structure into the cryo-EM density map of the phiKZ polysheath

1. Protein Identity and Related Structures Protein Identity & Related Structures

PHIKZ029

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/j0/3j0i/3j0i.fit
pddf	/app/data/pr_computation/j0/3j0i/3j0i.pr.out
profile	/app/data/saxs_computation/j0/3j0i/3j0i.dat