SAXSdb — 9bgm

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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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count	Chain A； UniProt 1–321 Chain D； UniProt 1–321 Chain G； UniProt 1–321 Chain J； UniProt 1–321 Chain M； UniProt 1–321 Chain P； UniProt 1–321 Chain S； UniProt 1–321 Chain W； UniProt 1–321 Chain Z； UniProt 1–321 Chain a； UniProt 1–321 Chain f； UniProt 1–321 Chain i； UniProt 1–321	Not recorded	gp83 head-to-tail × 12 （A0A2K8I0C0） gp80 portal protein × 12 （A0A2K8IC08）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9BGM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZDW Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins) Deposited 2025-11-26	Different experimental conditions 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
9ZE4 Asymmetric Tail Gating Complex of Pseudomonas Phage DEV Deposited 2025-11-27	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 1–321（321 aa） Chain B 1–321（321 aa） Chain C 1–321（321 aa） Chain D 1–321（321 aa） Chain E 1–321（321 aa） Chain F 1–321（321 aa） Chain G 1–321（321 aa） Chain H 1–321（321 aa） Chain I 1–321（321 aa） Chain J 1–321（321 aa） Chain K 1–321（321 aa） Chain L 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 8.50 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 D； PDBConstruct 1–321； UniProt 1–321 Author chain G； PDBConstruct 1–321； UniProt 1–321 Author chain J； PDBConstruct 1–321； UniProt 1–321 Author chain M； PDBConstruct 1–321； UniProt 1–321 Author chain P； PDBConstruct 1–321； UniProt 1–321 Author chain S； PDBConstruct 1–321； UniProt 1–321 Author chain W； PDBConstruct 1–321； UniProt 1–321 Author chain Z； PDBConstruct 1–321； UniProt 1–321 Author chain a； PDBConstruct 1–321； UniProt 1–321 Author chain f； PDBConstruct 1–321； UniProt 1–321 Author chain i； PDBConstruct 1–321； UniProt 1–321

gp83 head-to-tail

OrganismNot specified

UniProt A0A2K8I0C0

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count	Chain B； UniProt 1–244 Chain E； UniProt 1–244 Chain H； UniProt 1–244 Chain K； UniProt 1–244 Chain N； UniProt 1–244 Chain Q； UniProt 1–244 Chain T； UniProt 1–244 Chain X； UniProt 1–244 Chain b； UniProt 1–244 Chain d； UniProt 1–244 Chain g； UniProt 1–244 Chain j； UniProt 1–244	Not recorded	gp75 tail tube × 12 （A0A2K8I3N9） gp80 portal protein × 12 （A0A2K8IC08）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9BGM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZDW Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins) Deposited 2025-11-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain AA 1–244（244 aa） Chain AB 1–244（244 aa） Chain AC 1–244（244 aa） Chain AD 1–244（244 aa） Chain AE 1–244（244 aa） Chain AF 1–244（244 aa） Chain AG 1–244（244 aa） Chain AH 1–244（244 aa） Chain AI 1–244（244 aa） Chain AJ 1–244（244 aa） Chain AK 1–244（244 aa） Chain AL 1–244（244 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2K8I0C0_9CAUD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–244； UniProt 1–244 Author chain E； PDBConstruct 1–244； UniProt 1–244 Author chain H； PDBConstruct 1–244； UniProt 1–244 Author chain K； PDBConstruct 1–244； UniProt 1–244 Author chain N； PDBConstruct 1–244； UniProt 1–244 Author chain Q； PDBConstruct 1–244； UniProt 1–244 Author chain T； PDBConstruct 1–244； UniProt 1–244 Author chain X； PDBConstruct 1–244； UniProt 1–244 Author chain b； PDBConstruct 1–244； UniProt 1–244 Author chain d； PDBConstruct 1–244； UniProt 1–244 Author chain g； PDBConstruct 1–244； UniProt 1–244 Author chain j； PDBConstruct 1–244； UniProt 1–244

gp80 portal protein

OrganismNot specified

UniProt A0A2K8IC08

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 × 36 PDB declaration: 36-meric（36） Consistent with protein copy count	Chain C； UniProt 1–726 Chain F； UniProt 1–726 Chain I； UniProt 1–726 Chain L； UniProt 1–726 Chain O； UniProt 1–726 Chain R； UniProt 1–726 Chain V； UniProt 1–726 Chain Y； UniProt 1–726 Chain c； UniProt 1–726 Chain e； UniProt 1–726 Chain h； UniProt 1–726 Chain k； UniProt 1–726	Not recorded	gp75 tail tube × 12 （A0A2K8I3N9） gp83 head-to-tail × 12 （A0A2K8I0C0）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9BGM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9ZDW Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins) Deposited 2025-11-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain PA 1–726（726 aa） Chain PB 1–726（726 aa） Chain PC 1–726（726 aa） Chain PD 1–726（726 aa） Chain PE 1–726（726 aa） Chain PF 1–726（726 aa） Chain PG 1–726（726 aa） Chain PH 1–726（726 aa） Chain PI 1–726（726 aa） Chain PJ 1–726（726 aa） Chain PK 1–726（726 aa） Chain PL 1–726（726 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

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A2K8IC08_9CAUD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–726； UniProt 1–726 Author chain F； PDBConstruct 1–726； UniProt 1–726 Author chain I； PDBConstruct 1–726； UniProt 1–726 Author chain L； PDBConstruct 1–726； UniProt 1–726 Author chain O； PDBConstruct 1–726； UniProt 1–726 Author chain R； PDBConstruct 1–726； UniProt 1–726 Author chain V； PDBConstruct 1–726； UniProt 1–726 Author chain Y； PDBConstruct 1–726； UniProt 1–726 Author chain c； PDBConstruct 1–726； UniProt 1–726 Author chain e； PDBConstruct 1–726； UniProt 1–726 Author chain h； PDBConstruct 1–726； UniProt 1–726 Author chain k； PDBConstruct 1–726； UniProt 1–726

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	9bgm
Deposition date deposition_date	2024-04-19
Structure title title	Pseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins)
Keywords keywords	portal, tail hub, tail tube, complex, STRUCTURAL PROTEIN, gp75, gp83, gp80, 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	91.60 Å
Radius of gyration Rg (electron density) rg_electron	92.21 Å
Forward intensity I(0) i0	30283800000.00
Molecular weight molecular_weight	1457100.0 kDa
Excluded volume excluded_volume	1813500 Å³
Envelope volume envelope_volume	2989300 Å³
Hydration-shell volume shell_volume	285720 Å³
Envelope diameter envelope_diameter	442.8 Å
Shell Rg shell_rg	88.19 Å
Envelope Rg envelope_rg	91.67 Å
Shape Rg shape_rg	92.25 Å
Total Rg total_rg	92.07 Å
Total atoms total_atoms	102504
Residues n_residues	13212
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	263.4 Å
Rg (real space) rg_real	85.41 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	2.8890e+10
I(0) uncertainty (real space) i0_real_error	5.6330e+08
Rg (reciprocal space) rg_reciprocal	87.56 Å
I(0) (reciprocal space) i0_reciprocal	29920000000.0000
Solution quality estimate total_estimate	0.9077
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	108.4 Å
Skewness Skewness skewness	0.502
Kurtosis Kurtosis kurtosis	0.031
Angular range angular_range	— – 0.0850 Å⁻¹
Current regularization parameter α current_alpha	0.6235
Highest regularization parameter α highest_alpha	2048000000.0000
Real-space data points n_real_points	18
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.020; Oscil: 0.886; Stabil: 0.986; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.248

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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,A,D,G,J,M,P,S,W,Z,f,i
Atom count atom_count	102552

MAVEPITIADLTEVKLDGKGALDQLLQVTRLHLAKEHDAGRLKGQEYAAVLTGGITAVLQNAVMFLLQKDEAANKAALVEAQIKLTEKQGELLDKQIAQADKDAELIAAKVKLTLEQAKLPDSQIRSAGFQDLLVQEQTKVQTAQTRRIDQEILSAGFQDLLVKEQTAKTKQDVLTAVQQTKVMEQQVLESTQKVLNMKQELLNLVAQECLLKAQFDLTKDQGLNTQEQTILVRQKVASERAQTIGAGVDADSVIGRQKELYKAQADGFKRDAEQKAAKILIDTWNVRRTTDTGTQANTTNRLDDANVGRVVNMLMTGVGA

Entity 2 Entity 2 polymer

Description description	gp83 head-to-tail
Molecular weight formula_weight	27868.9 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	b,B,E,H,K,N,Q,T,X,d,g,j

MTIQLKQVIDLLAEGELSNIKYVNIDTGALVLERVPSLIRAINLGVLDLHKRFLLKEGMLKIQLEEGRRLYPLRPAYQVGQKPKPGVPQFITEGNKLGRQSILKIEKIIGDNGVEYYLNDTWQPLNITTPEFDVLEISDEFYCHSSSKTLEVRYRRAPTPMKICVDNLDSWGCIDIDLPYTHLQALLYFVASRCQTPIGFMENTAQEGFNFSQKYEAECANLDAQNLRIDPVGNQDRFTRGGWV

Entity 3 Entity 3 polymer

Description description	gp80 portal protein
Molecular weight formula_weight	81739.5 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,C,F,I,L,O,R,V,Y,e,h,k

MADVDEDYLTLPNEDGDPSKRLQPEWSNAPSLAQLKQDYQEAKQVTDEKITQINRWLDYMHVRGEGKPKTEKGKSAVQPPTIRKQAEWRYSSLSEPFLSSPNIFEVNPVTWEDAESARQNGLVLNQQFNTKLNKQRFIDEYVRAGVDEGTIIVKVGWNYQSRTVKEQVVTYEMMPDSSEELAQIYQTAAQIREESPSEYPEIPEDVRLGLEETEANGIQVRAVPVGSEEEEREETVENHPTVQVCDYNNIVIDPSCGSDFSKAKFLIETFESSYAELKADGRYKNLDKIQVEGQNLLSEPDYTGPSEGVRNFDFQDKSRKRLVVHEYWGYYDIHGDGVLHPIVATWVGAVMIRMEENPFPDKKIPYVVVSYIPRKRDLYGESDGALLIDNQRIIGAVTRGMIDTMARSANGQVGVMKGALDVTNRRRFDRGENYEFNPGADPRAAVHMHTFPEIPQSAQYMINLQQAEAESMTGVKAFNAGISGAALGDTATAVRGALDAASKRELGILRRLSAGIIEIGRKIIAMNAEFLDDVEVVRITNEHFVDIRRDDLAGNFDLKLDISTAEEDNAKVNDLTFMLQTMGPNMDPMMAQQIMGQIMELKKMPDFAKRIREFQPQPDPIAQQKAQLELMLLQAQIEAERARAAHYMSGAGLQDSKVGTEQAKARALASQADMTDLNFLEQESGVQQARKRELQQAQSEAQGKLAMLNSQLKRLDEATSARTSQK

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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	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	3228

fit	/app/data/saxs_computation/bg/9bgm/9bgm.fit
pddf	/app/data/pr_computation/bg/9bgm/9bgm.pr.out
profile	/app/data/saxs_computation/bg/9bgm/9bgm.dat

Pseudomonas phage DEV neck and tail (portal, head-to-tail and tail tube proteins)

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

gp83 head-to-tail

State in the Current Structure

Other States of the Same Protein in the Database

gp80 portal 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)