SAXSdb — 9vvp

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1. Structure Basics

entry_id	9vvp
deposition_date	2025-07-16
title	Core proteins of the bacteriophage E1004
keywords	Complex, 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	76.57 Å
rg_electron	75.91 Å
i0	22026200000.00
molecular_weight	1214400.0 kDa
excluded_volume	1501400 Å³
envelope_volume	2731900 Å³
shell_volume	278910 Å³
envelope_diameter	231.2 Å
shell_rg	90.21 Å
envelope_rg	73.08 Å
shape_rg	75.89 Å
total_rg	76.12 Å
total_atoms	85296
n_residues	10989
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	284.7 Å
rg_real	79.85 Å
rg_real_error	1.88 Å
i0_real	2.2030e+10
i0_real_error	4.5850e+08
rg_reciprocal	78.05 Å
i0_reciprocal	22110000000.0000
total_estimate	0.8781
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	99.7 Å
skewness	0.472
kurtosis	0.612
angular_range	— – 0.1000 Å⁻¹
current_alpha	0.9588
highest_alpha	2407000000.0000
n_real_points	21
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.622; Stabil: 0.888; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.935

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Gp17
formula_weight	7814.8 kDa
src_method	nat
entity_count	16

Polymer

type	polypeptide(L)
strand_id	S,E,F,A,G,B,C,D,c,d,e,f,g,h,i,H
atom_count	85296

MCFSPKISTPKPSVQAPEPAPLSEEVASVDIGAESDVDTNETKGIKDLKVKKESAPKDKSSVSRAMRNSGVNMG

Entity 2 polymer

description	Gp28
formula_weight	85342.8 kDa
src_method	nat
entity_count	8

Polymer

type	polypeptide(L)
strand_id	I,V,Y,K,a,Q,T,N

MASNIESALANRTMGRGRAPGKTIAVNYQAASVQAPTGDSGLARALTSFVESGTGLYKQFKDEEKTRADERSNEIIRKLTPQQRREAIQNGTLLYQDDPYAMEALRVKTGRNAAFAVDDEINVKIQNGEFRTRQDMEEYRHQRLQDAAKSYAEEAGINPTDEFFQRGFNDNITDRNIAIYGSFNKYFSKQSEETAMLNTRIEMNSFLNDGDLMRSPESGKTFMAYLRDGLTTAAIPSDQRAREVITQTVRDAIQKSGGSNFLQQVRGERITLNGVDATVEEIVGPDVFNAAIVEAQGTEYKLVAKYQEDLALGVQSAILQDDPTIGLAQIQKLKEQNNLLQPGEELTPQRQMLINAEASLLEAVKRKSAEQAKENTKLIQTQNKQLVIDQVYQRRLAGDNVSTNYEDLPVSEATGEFKRSDMNNYASAKLQQIDQMDIPEAAKDAQKVALLRADTNNGPFRNAFQTLTQDAAGEWQAAVIRGQYDPDKMQRFESLRRAYTQDPSSFAALYPDQAQLFSTFDQMDKIGLDPQTMIEADKQAASQSREMRMESDKAWQELKNDSRNKDLSRLPTSLDASARKVWDSWYYRTGNADAATQQTQRWLNENTVTFQSEGSDGKSIGMVSKHQLMVGDNPESWQVGRDIIDTARKQLIKANPWVVNSQLSVVEQNGSIFLQDATGTIRIRYDKELVGKLYREQQQKAQDAAYAQAERDANKRARIVGTKAAGDKRRADREANIEKRGGMYNDVSLEGIAKVLIGKE

Entity 3 polymer

description	Gp27
formula_weight	20326.7 kDa
src_method	nat
entity_count	8

Polymer

type	polypeptide(L)
strand_id	J,M,P,j,U,X,Z,b

MCEPVSIGLGIMSVAGATMSASQQAKAEGAAIDAQNRQAQEMIKQMNYSDANLKMQERDLKEQQMAELTETTLNGIRNQGMVRAAVAESGLEGNSMDRIERQVAGDTVKERAGITESYNRDYAAIFGNRIANIENTQSAIRGQGKIIKTSPLAHALNVATAGVQGYAAGKSMSGTSGSGGAAPISAAKGTPTGHS

Entity 4 polymer

description	Gp29
formula_weight	141116.8 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	L,O,R,W

MATRGIRNNNPGNIRVSKDQWEGMTGDDGAFVTFDSPESGVRALGKNLLSYGRQGYDSIEKIINRWAPPNENDTKAYIDSVVAATGIPATQSLDLSNQDTLSALAQAISFHETGSRYDPEVYQKGVARALNGISPKTPPVSANVFDALTEGLKAKPKVALGENLPTAAGLNIEGQAPEAPNESFGEMFYKSTGETMQEREDRSTWFGFGAATEAEVKNSMVGVAIRAGQTEDSLDVIGDVFNPTRWNNHKWTREELDQIRNAGVLPQYYGVITGGSPQNLTELINLALENQKLDQEKAKAGTGAQLAAGVIGAGVDPLTYVPIAGQVGKGGKLVNKMFTVAAQSGALAGVSEMARTSVAGGDAHVAEAILGGALFGGGMTAIADGLGRALGRNTNEFAGPATRLEARETARNVDGQDLSRLPIQEGEQTFSHQGVKFADVPNEPGSVRLEDGSILIGENPLNPKTRQVFDEVIEPERAAAGVNLGGLTEIGLKLLRSENPEIRGVAADLVRSPTGMQSGASGKIGTTASDVFERLRAVDHRFYNDIDDAVTEALKDPYFQTAFWRDSGAFRQDIYQRVSMAIEDGSGNLKAELTPGELKVYDLLKNQFDAKREMMENPAMFGRPDAQSIFPGSRFKGTYVPHVYSSQMKELYIKELGSPEALQEAIKKSWLTSYASRPEVKKRVDEALLEADPTLTPEGLAAAVDKYANDKAYGISHTEQFERSSVMEENINGLVGLENNSFLEARNLFDSDMSIVLPNGQTFSVNNLREWDMDKIVPAYNRRVNGDIAIMAGTGKTTKEMKDLVETLMNKAGDDGKLKGEVSTLRDTLKILTGRARRDGADDAAFATVMRTMTDLAFFAKNAYMGVQNLTEIGGMLARGNVRAMLHGVPMFRDLAFRNKKVGASEIKDLHNVIFGKELDDSIRPSKQDVIDRLRSYSDLGRGAATALGTAKYYTGELAVRSPFTKVLNGTTNYLLDAGRQGFLSDIVEHSLTGSKRRFDDRWLKTAGISDEQWKGIKSLIRESVTRGPDGKYTIKDKKAFSQDQRAMDLWRMGDTIADETLLRPHKLSNMDAKAYGPIAKTVLQFKNFVIKSINGRTMRTFYNATKNNRAMDAALSTVMSMGLAGMYYMAQAHIKAYAMQDGRDREYLKQALNPTMIGYAALSRSSHLGGPLGVANILGGIAGYEDTKMLRSSILPRSPTEKTEKPIAFGAASSGPVMNVVGNFLEQVPAFGYAANVGATAYNLAGYLKADTRVNERDYMTGMYNTFRELVPNDPITQKLLLGTFEEQGIHIKD

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6. Citations (1)

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resolution	3.330 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.33 Å
resolution_method	—
num_particles	32932

fit	/app/data/saxs_computation/vv/9vvp/9vvp.fit
pddf	/app/data/pr_computation/vv/9vvp/9vvp.pr.out
profile	/app/data/saxs_computation/vv/9vvp/9vvp.dat

Core proteins of the bacteriophage E1004

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)