SAXSdb — 9vzk

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1. Structure Basics

entry_id	9vzk
deposition_date	2025-07-22
title	Cryo-EM structure of bacteriophage P1 baseplate in C3
keywords	baseplate, phage, VIRAL PROTEIN; VIRAL PROTEIN
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.65 Å
rg_electron	60.61 Å
i0	2617290000.00
molecular_weight	440270.0 kDa
excluded_volume	554990 Å³
envelope_volume	930490 Å³
shell_volume	127920 Å³
envelope_diameter	236.7 Å
shell_rg	61.96 Å
envelope_rg	60.53 Å
shape_rg	60.61 Å
total_rg	60.62 Å
total_atoms	31051
n_residues	3944
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

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3. P(r) Analysis (GNOM)

dmax	207.9 Å
rg_real	60.54 Å
rg_real_error	1.57 Å
i0_real	2.6170e+09
i0_real_error	5.5100e+07
rg_reciprocal	60.70 Å
i0_reciprocal	2618000000.0000
total_estimate	0.8725
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	72.0 Å
skewness	0.308
kurtosis	-0.275
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0007
highest_alpha	281600000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.901

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Gp6
formula_weight	37261.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	31051

MATKTTTAPETDSKRTQLFLQSVSIGQNEIPREMIVGCTYVEPGELSGPQLMLMIRDSTAYVVNKLGVKFGTILTVSLGDPEGHGGILFSEEFFVLKAPRKDDTVLIYAFSNPVRLLKVPSTSAQYFVDKPPSAVVSSLAPGLKVNADSFRKTSTYHLNVGEKPTKVLQEIARDTGSMCWASRGMINFKSMEKMANAAPSLTYESANPNTSGFTISQFNILNADYEYQRRHNYRMASYDMTKGVVYSGNQEDPIKFTSNPDPTALANYNKFILPRLDMLVEGNAALTPGTTLKIVVHNTAGDGELDESIPDKMIVMSVTHFEDRFRFVSRAQLGVVNG

Entity 2 polymer

description	PmgG
formula_weight	20578.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	2,C

MAPIAYGVYSQADGVSPYLKVTLTNSQYQVTGYISQGAAMNMAQNWEAPFTGMSMGSVSGALGGFVQVGTETTSVARWNSLMVWEGGTPPTFTLPVTFIALNNPFIEVSGAIAALTAMISPELKAANVGGQIPERVTLNIGRRINITDVAIQDLSFDLDAPRDSNGYFLKNTVNLQLTGSSIYNSSDIVRAFQ

Entity 3 polymer

description	PmgA
formula_weight	13249.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,K

MANNNEIDPLLTLELSGVKTYESQEEAWGARLYEWLNTYQGEVYGDPSWGNVLPQFKHEPTNLSHVQIAVEAMLLQKLTVDLPDIPISGLSVAEGDAFDKLKISIRIRDITITQDVVL

Entity 4 polymer

description	Tub
formula_weight	22335.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,O

MGLNVASVKSYVSSALTTTLFGSGVGEREVGKLTSIIMNKMLFAQGWQFSVEVDGLEGADFFAKDITYHDYSIEYETIKIGGGNILQPTERSPGQITMMVRDTVDGLVLDWFKTAKSRVINPDGTGNIPSQYLLNVRIYRLLSSGLTKLENEMTVFPVTTGDVTYARDQVTEFKSFPMTFALHSTFNQSSSSLASLLGFSFSL

Entity 5 polymer

description	BplA
formula_weight	53624.3 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	T,Y,f,g

MSKTTPTKDSIRAEFEELVEKDSFWSKFVGSQFVSMLTLFITQIVYRCFQYADAALAEGFISTATRRSSILAAAETNSYVGTKPTPSSGMIEITATSEDAPAVIPKNMPLISDDQYPYMTMDVCRLVDGTGTVEVAQLEIQEVTYTVTAAKEFLEVVLSKALTAVCYKLEVFVTTDGKTTQWSSSTMFRLAGSKSQVYVEFYKPSEQLGVRFGDGLIGQIPPEGSTITLKVWCTNGDITLVAGQNLTPVDSAANLANLISVKTTTPITAGTDAETTEITRNRAQYYLAYDDQVVWGGDYTYFLVRNIPGLSWVKAWGEGQQEKLDGAYNVQNINKIFISGWHPNKSQSELEEMILAAFKKVPNELNKKFSYKEVRKLPFKITITGRISASLTIENVTDELKSALETKFGRDSTFFDPNRVGKYILIKKKDVWAFIETLGYFRDFYLEFVEWNESNGFYDFVYLDTENSTFNISYEEE

Entity 6 polymer

description	Gp26
formula_weight	14472.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	d,t

MATSITTTQSTRQYPLSRYDDRNIADPILRAELRKEVMLMCESNDKNLTIYYVLPDEQYRPDLLAYRMWGIAELRWVVTLAAGLEDESQGMTVGKKLKLPPATWIREMIRHFQYDGQVIGTLSIA

Entity 7 polymer

description	Gp16
formula_weight	31387.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	k,w

MQRSWFNHRLTSAKQKSLLYKSLADLVQSMMDTFVDPWLERITNRKSIFSMSKEDLETRTNELGQFFTIRTSNSSSVPMLLQQRLDEIHFKGTERPINQTIYREFNGISVLWDPIYAPVDLERHPYGTVLIPESTLETTGGTFGEMFLTSRGMISIPINDLARTMGITGTIDQSAITEEILRKFNQFVKPLLPLHIVFDGLTLYLSVVVNEHADMITLNEISDTEKAYCWFETSDTTSLTGVTSISAPITATPGGTIVKATPTFDRTRADDLLLDSDA

Entity 8 polymer

description	Gp5
formula_weight	21687.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	q

MGSLTGKYRAVVISVDDPKGLMRTQIRVVGMMDGLPDASLPWAEAILSNANTFSPFLPGDKVWVEFPYNGDSRWPLIIGYAQDASGGAPNVPPEASGQGEGYVPPEVEGAPAQPSTSAKKDFISSRNGLMEIRTAGGAWAVTHLKSGTTIGFNEAGELYAISQGPAFISSAGNLDIKSGADVALKAGGSMAIEASGNLSIKAAQVSVDKA

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6. Citations (1)

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resolution	3.20 Å
resolution_method	—
num_particles	30339

fit	/app/data/saxs_computation/vz/9vzk/9vzk.fit
pddf	/app/data/pr_computation/vz/9vzk/9vzk.pr.out
profile	/app/data/saxs_computation/vz/9vzk/9vzk.dat

Cryo-EM structure of bacteriophage P1 baseplate in C3

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)