← Back to search

9zdw

Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins)

Method: ELECTRON MICROSCOPY D_max: 243.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9zdw
deposition_date	2025-11-26
title	Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins)
keywords	bacteriophage, virus, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	84.61 Å
rg_electron	84.69 Å
i0	27636900000.00
molecular_weight	1397100.0 kDa
excluded_volume	1741000 Å³
envelope_volume	2763200 Å³
shell_volume	273660 Å³
envelope_diameter	383.6 Å
shell_rg	86.38 Å
envelope_rg	84.25 Å
shape_rg	84.74 Å
total_rg	84.51 Å
total_atoms	98304
n_residues	12636
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	243.2 Å
rg_real	79.08 Å
rg_real_error	1.05 Å
i0_real	2.6350e+10
i0_real_error	5.7690e+08
rg_reciprocal	82.49 Å
i0_reciprocal	27470000000.0000
total_estimate	0.9125
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	94.6 Å
skewness	0.404
kurtosis	0.007
angular_range	— – 0.0900 Å⁻¹
current_alpha	0.6871
highest_alpha	2058000000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 0.889; Stabil: 0.987; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.285

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	gp80 portal protein
formula_weight	81739.5 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	PA,PB,PC,PD,PE,PF,PG,PH,PI,PJ,PK,PL
atom_count	98304

MADVDEDYLTLPNEDGDPSKRLQPEWSNAPSLAQLKQDYQEAKQVTDEKITQINRWLDYMHVRGEGKPKTEKGKSAVQPPTIRKQAEWRYSSLSEPFLSSPNIFEVNPVTWEDAESARQNGLVLNQQFNTKLNKQRFIDEYVRAGVDEGTIIVKVGWNYQSRTVKEQVVTYEMMPDSSEELAQIYQTAAQIREESPSEYPEIPEDVRLGLEETEANGIQVRAVPVGSEEEEREETVENHPTVQVCDYNNIVIDPSCGSDFSKAKFLIETFESSYAELKADGRYKNLDKIQVEGQNLLSEPDYTGPSEGVRNFDFQDKSRKRLVVHEYWGYYDIHGDGVLHPIVATWVGAVMIRMEENPFPDKKIPYVVVSYIPRKRDLYGESDGALLIDNQRIIGAVTRGMIDTMARSANGQVGVMKGALDVTNRRRFDRGENYEFNPGADPRAAVHMHTFPEIPQSAQYMINLQQAEAESMTGVKAFNAGISGAALGDTATAVRGALDAASKRELGILRRLSAGIIEIGRKIIAMNAEFLDDVEVVRITNEHFVDIRRDDLAGNFDLKLDISTAEEDNAKVNDLTFMLQTMGPNMDPMMAQQIMGQIMELKKMPDFAKRIREFQPQPDPIAQQKAQLELMLLQAQIEAERARAAHYMSGAGLQDSKVGTEQAKARALASQADMTDLNFLEQESGVQQARKRELQQAQSEAQGKLAMLNSQLKRLDEATSARTSQK

Entity 2 polymer

description	gp75 tail tube
formula_weight	35267.2 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	TA,TB,TC,TD,TE,TF,TG,TH,TI,TJ,TK,TL

MAVEPITIADLTEVKLDGKGALDQLLQVTRLHLAKEHDAGRLKGQEYAAVLTGGITAVLQNAVMFLLQKDEAANKAALVEAQIKLTEKQGELLDKQIAQADKDAELIAAKVKLTLEQAKLPDSQIRSAGFQDLLVQEQTKVQTAQTRRIDQEILSAGFQDLLVKEQTAKTKQDVLTAVQQTKVMEQQVLESTQKVLNMKQELLNLVAQECLLKAQFDLTKDQGLNTQEQTILVRQKVASERAQTIGAGVDADSVIGRQKELYKAQADGFKRDAEQKAAKILIDTWNVRRTTDTGTQANTTNRLDDANVGRVVNMLMTGVGA

Entity 3 polymer

description	gp83 head-to-tail
formula_weight	27868.9 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL

MTIQLKQVIDLLAEGELSNIKYVNIDTGALVLERVPSLIRAINLGVLDLHKRFLLKEGMLKIQLEEGRRLYPLRPAYQVGQKPKPGVPQFITEGNKLGRQSILKIEKIIGDNGVEYYLNDTWQPLNITTPEFDVLEISDEFYCHSSSKTLEVRYRRAPTPMKICVDNLDSWGCIDIDLPYTHLQALLYFVASRCQTPIGFMENTAQEGFNFSQKYEAECANLDAQNLRIDPVGNQDRFTRGGWV

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	64223

fit	/app/data/saxs_computation/zd/9zdw/9zdw.fit
pddf	/app/data/pr_computation/zd/9zdw/9zdw.pr.out
profile	/app/data/saxs_computation/zd/9zdw/9zdw.dat

Pseudomonas phage DEV delta-gp53 mutant neck and tail (portal, head-to-tail and tail tube proteins)

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)