SAXSdb — 9ze4

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

gp75 tail tube

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 heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–321 Chain B； UniProt 1–321 Chain C； UniProt 1–321 Chain D； UniProt 1–321 Chain E； UniProt 1–321 Chain F； UniProt 1–321 Chain G； UniProt 1–321 Chain H； UniProt 1–321 Chain I； UniProt 1–321 Chain J； UniProt 1–321 Chain K； UniProt 1–321 Chain L； UniProt 1–321	Not recorded	N4 gp53-like protein × 1 （A0A2K8HNE9） Tip attachment protein J central straight fiber domain-containing protein × 3 （A0A2K8HW65）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 8.50 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 9ZE4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9BGM Pseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins) Deposited 2024-04-19	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain A 1–321（321 aa） Chain D 1–321（321 aa） Chain G 1–321（321 aa） Chain J 1–321（321 aa） Chain M 1–321（321 aa） Chain P 1–321（321 aa） Chain S 1–321（321 aa） Chain W 1–321（321 aa） Chain Z 1–321（321 aa） Chain a 1–321（321 aa） Chain f 1–321（321 aa） Chain i 1–321（321 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ZDW Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins) Deposited 2025-11-26	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain TA 1–321（321 aa） Chain TB 1–321（321 aa） Chain TC 1–321（321 aa） Chain TD 1–321（321 aa） Chain TE 1–321（321 aa） Chain TF 1–321（321 aa） Chain TG 1–321（321 aa） Chain TH 1–321（321 aa） Chain TI 1–321（321 aa） Chain TJ 1–321（321 aa） Chain TK 1–321（321 aa） Chain TL 1–321（321 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2K8I3N9_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–321； UniProt 1–321 Author chain B； PDBConstruct 1–321； UniProt 1–321 Author chain C； PDBConstruct 1–321； UniProt 1–321 Author chain D； PDBConstruct 1–321； UniProt 1–321 Author chain E； PDBConstruct 1–321； UniProt 1–321 Author chain F； PDBConstruct 1–321； UniProt 1–321 Author chain G； PDBConstruct 1–321； UniProt 1–321 Author chain H； PDBConstruct 1–321； UniProt 1–321 Author chain I； PDBConstruct 1–321； UniProt 1–321 Author chain J； PDBConstruct 1–321； UniProt 1–321 Author chain K； PDBConstruct 1–321； UniProt 1–321 Author chain L； PDBConstruct 1–321； UniProt 1–321

N4 gp53-like protein

OrganismNot specified

UniProt A0A2K8HNE9

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 heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain M； UniProt 1–740	Not recorded	gp75 tail tube × 12 （A0A2K8I3N9） Tip attachment protein J central straight fiber domain-containing protein × 3 （A0A2K8HW65）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 8.50 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A2K8HNE9_9CAUD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–740； UniProt 1–740

Tip attachment protein J central straight fiber domain-containing protein

OrganismNot specified

UniProt A0A2K8HW65

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 heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain N； UniProt 1–429 Chain O； UniProt 1–429 Chain P； UniProt 1–429	Not recorded	gp75 tail tube × 12 （A0A2K8I3N9） N4 gp53-like protein × 1 （A0A2K8HNE9）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 8.50 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A2K8HW65_9CAUD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–429； UniProt 1–429 Author chain O； PDBConstruct 1–429； UniProt 1–429 Author chain P； PDBConstruct 1–429； UniProt 1–429

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	9ze4
Deposition date deposition_date	2025-11-27
Structure title title	Asymmetric Tail Gating Complex of Pseudomonas Phage DEV
Keywords keywords	virus, bacteriophage, receptor-binding protein, VIRAL PROTEIN; VIRAL 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	119.30 Å
Forward intensity I(0) i0	3815300000.00
Molecular weight molecular_weight	509720.0 kDa
Excluded volume excluded_volume	633890 Å³
Envelope volume envelope_volume	1145300 Å³
Hydration-shell volume shell_volume	106920 Å³
Envelope diameter envelope_diameter	428.9 Å
Shell Rg shell_rg	61.55 Å
Envelope Rg envelope_rg	117.10 Å
Shape Rg shape_rg	119.40 Å
Total Rg total_rg	118.20 Å
Total atoms total_atoms	35853
Residues n_residues	4951
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	305.7 Å
Rg (real space) rg_real	105.80 Å
Rg uncertainty (real space) rg_real_error	2.37 Å
I(0) (real space) i0_real	3.6540e+09
I(0) uncertainty (real space) i0_real_error	8.6090e+07
Rg (reciprocal space) rg_reciprocal	92.24 Å
I(0) (reciprocal space) i0_reciprocal	3560000000.0000
Solution quality estimate total_estimate	0.8330
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.5 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.940
Angular range angular_range	— – 0.0650 Å⁻¹
Current regularization parameter α current_alpha	0.1404
Highest regularization parameter α highest_alpha	80630000.0000
Real-space data points n_real_points	14
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.015; Oscil: 0.564; Stabil: 0.958; Sysdev: 1.000; Positv: 1.000; Valcen: 0.838; Smooth: 0.430

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	gp75 tail tube
Molecular weight formula_weight	35267.2 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	35853

MAVEPITIADLTEVKLDGKGALDQLLQVTRLHLAKEHDAGRLKGQEYAAVLTGGITAVLQNAVMFLLQKDEAANKAALVEAQIKLTEKQGELLDKQIAQADKDAELIAAKVKLTLEQAKLPDSQIRSAGFQDLLVQEQTKVQTAQTRRIDQEILSAGFQDLLVKEQTAKTKQDVLTAVQQTKVMEQQVLESTQKVLNMKQELLNLVAQECLLKAQFDLTKDQGLNTQEQTILVRQKVASERAQTIGAGVDADSVIGRQKELYKAQADGFKRDAEQKAAKILIDTWNVRRTTDTGTQANTTNRLDDANVGRVVNMLMTGVGA

Entity 2 Entity 2 polymer

Description description	N4 gp53-like protein
Molecular weight formula_weight	82267.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

MGLFSSKKKTVVNTTVQRVFDDAHIPDSPRTGVIQGITHETGIVENILEKLSDSIGVRANTAYLWAQRNNYYWGLPESKVVNGVDARTVVVQTIARSEGTITTYYNQFGPLNSLHWGFTELVRLYQYNPLTNELPGLSTTKGSKVYLFDMIPVFQTDTVAWADETANKGMLQDFGFSPKSGYTPSRPYNTIGGMGQFAGWSPYRTDNSFGEDYVLLTYEWKDAQGVIKQETIRMIMNLDLSLDYHQVRFRRQNGTQGFFTYQDGKGTYPLIDGVFNLDYTKQGTYYPWMYCRFNKMNVKDIPGNAYKDVKEVAKISGIGIDELIDGVHADPDIGDVAQVVLFYGVPPGATNQDQLTYIFEYLLLLHSEALAQIQKAENLQGKLGDYSNTADQMITMRDKYFKMDFSFSGITVNRKSGKVGPIGFINVKSGMADKSSGQIKTQQPAYTYTRQAMDSMYDEVIIYNPAMHYQITSKKGHVAQLGQPELLIPVDRVVLSQLGLRAQEQLLCRSLHMAINTQVQIKTPWYASGFFKVILIVVAVAVTIFTAGSAWGTIVAAASLGVAALTMVIVQMIVTTLAVSYGVKLFVRAVGPELGILAAVAALAVGAYGMSNNATWSENLMAVSHGIAKESQTMEQAGLMDTLKELERNQTYYADQLQSLEDQRRELGLVQFQALQGEDFVNRPLTILGESTDDFFSRTVHAGNIGAASFQLTEYFVDAKLQLPSINETIEEINNGLSVQ

Entity 3 Entity 3 polymer

Description description	Tip attachment protein J central straight fiber domain-containing protein
Molecular weight formula_weight	46398.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,O,P

MVDTCNINGVCGTGDWNGPKPGDPNMNDLLLKATPAFGGIDIEFTWPTTNPGAVGTTRLFRSTDANFAGATIRAFVNGNFYFDKTDPGSKVDQRYYYWIQLVSINGTDGDIIGPATATARPLIEQMIEQLTGEIDNGLLSQELRQEIAQIELNKLGITQEEIERAKNDDALGVRLTQIDAKMDQNTAILQEEVRARVTADSSLVQTVNTMYADFNGNIAAIQQENTALATKVNALASSVTTINATVNGDSASGKVGLVAEVQTLDGKVTQIGARWTATVDVNGLVGGFGVYNDGRTVEAGFNVDRFWIGRPGTPKNPGSYPFIIDNNIVYIKEAAIQKLTFDKLRAQDGSFIVQNGKIQADYIEAKDIVVNNIQSDNYQPGVQGWAFRPNGIMEINGTAGTGRMTINNATIKVFDQAGKLRVHIGNLQA

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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	—

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

Resolution resolution	8.50 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	8241

fit	/app/data/saxs_computation/ze/9ze4/9ze4.fit
pddf	/app/data/pr_computation/ze/9ze4/9ze4.pr.out
profile	/app/data/saxs_computation/ze/9ze4/9ze4.dat

Asymmetric Tail Gating Complex of Pseudomonas Phage DEV

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

gp75 tail tube

State in the Current Structure

Other States of the Same Protein in the Database

N4 gp53-like protein

State in the Current Structure

Other States of the Same Protein in the Database

Tip attachment protein J central straight fiber domain-containing protein

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)