SAXSdb — 9v7k

▼

1. Structure Basics

entry_id	9v7k
deposition_date	2025-05-28
title	Phycobilisome allophycocyanin hexamer C from Gloeobacter violaceus PCC 7421
keywords	Phycobilisome, PHOTOSYNTHESIS; PHOTOSYNTHESIS
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	40.28 Å
rg_electron	39.57 Å
i0	910302000.00
molecular_weight	254100.0 kDa
excluded_volume	320470 Å³
envelope_volume	400650 Å³
shell_volume	79959 Å³
envelope_diameter	137.3 Å
shell_rg	48.77 Å
envelope_rg	39.18 Å
shape_rg	39.55 Å
total_rg	40.07 Å
total_atoms	17887
n_residues	2269
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	126.8 Å
rg_real	40.09 Å
rg_real_error	0.80 Å
i0_real	9.1030e+08
i0_real_error	1.4790e+07
rg_reciprocal	40.27 Å
i0_reciprocal	910500000.0000
total_estimate	0.8956
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	48.8 Å
skewness	0.155
kurtosis	-0.501
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	157900000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.950

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (7)

Entity 1 polymer

description	Phycobiliprotein ApcE
formula_weight	130002.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	17887

MSIRGTSGSTVARPRLFRTVMTETINGINAEDRYPNSGEVSQLDQFFGDGQRRIAIVAKLTENAEMIVSRAANRIFVGGSPMAYSERQKAKAKSPLANDEFGNEPIVEDRGGFLESLKSIFSTRGGGGRASADFAVPPDFEPINIARYGPERMQKSIRDLDWFLRYTTYAILAGDPSILEANCLGLREILEKSCSISATIVALLEMRKNAARLFKDEADSKLVSSYISVVIRALDADRSDAPADIVRPSSEDRPGLTLPYIYKLSADSLTTFKMTAIYGADGRPKVNLSSDEKERVVRAAYRQVFERDLKAYGQSVSEAESKVKNGEISVREFVRRLGKSELYRREFYQPFINSRVLELAFKHFLGRAPESRAEVQKYFSIISSPIVRGQSSMPSGGLYALIDALIDSEEYTSIFGEDTVPYLRNLGVEAQPSWNWGAAYDLYNYAAPRRKVPQFITLFADYTQPLPNQHPYGAGNDPLEIQFGAIFKNSTINPAERAAPIGKDVKRILIRNGSPTSNERGNPTGMSEGATTLGPKIFKLTQNVGFRSKGMVQNAGVVTVEGSVQALITAAYQQIFGRQLYQGQRLKVAEIKLENGETTVKEFVRALGRSEIFRKLYWEPFYVCKAIEYIHRRLLGRPTYDRVENNRYFDIASKKGFYGVVDAMLNSNEYQEVFGEDVLPYERYLTPAGLSLRKGRFGSSDVLTTPGGITPRGDAARMMDKIQELGTPINERSIPEMYVNQGVPALKRQRKVFKQSQATDRESFDALVTAAYVQVFDKDIASYIRSEFSALESRLRNRETSVKEFVRLLGFSALYRKQFHDRYPNTKVVEFAFKHFLGRAVKNQAELIKYHGLLGRKGIKALIGALVDGEEYGRLYGEDTVPSWQFPTLPAANYPNSVELYNRFTRQDDSLVVPSFKPIRSKMDIASMPLVQAALKEQQATKTALDMSRPMFLELGRSFKGADGQSVEVGVGTLRRQLEHIYRIAPDATRSEKDVAINAIYRQVLDVFAGIPPSYLRLSEAESKLKNNEISVREFVRRLGRSENYRKRFFEPYSSPKVVELLTKHFLGRAPISQQEISTYVQILGTKGLAAAVDAIVESPEYLTIFNEDIVPYRRYPTLPAGNYRASVRVNDEELISQSWSSLSPTYTGYQYVTR

Entity 2 polymer

description	Glr1262 protein
formula_weight	92127.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MSTVLDDQSKAYAPGSANGPTAGLEPFVRMSRMIRSGVPEDREEPDELWLSMVRDIFGRGYMDRLSQTRAIDYSAFVRPADQATADGAAQTKLGITAIAPDQGVELRPNFTEADVITVIRAAYKQLFGNTYILESERVIQAESLLRNGSISVREFIRILAKSDLYKERFFRCTSNNRFIELNLKHLLGRAPYNQGEIAEHLDRYCQSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQSAAAFERMRALYSGDAGSDTDRNQNGQRTELTSGLADPAQPVRARTDYALTRVDIPGGNGAAGRLAALDESLGSWLDAARDLISQNDYSQKAIEVEPKRVAPYAQYLTPAVEATPDAAAQTKLGITAVAPDQAVELRPNFGEAEVQAVIRAAYKQIFGNTYILEADRVVIAESLLRNGSISVREFVRLLAKSDLYRDRFFRTASNNRFIELNFKHFLGRAPYSQAEIGEHFNRYHKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQAARGFDQMQQLFAGDAGSDTDRGIGAQPAAKLTFPLSRPLGVTSAYFPSSQGGAATSDGLEMFTRMARELTVTPVSARRTTSPTAPTAPAMPLAGYYSRPAPRATADGDAQTKLGITAVAPAQAVELRPNFGETELQAVIRATYKQLFGNTYILEADRVVQAESLLRNGSINVREFVRLLAKSELYKERFFHCTSNNRFIELTFKHLLGRAPYNQSEFVEHLDRYQKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQTGQAAGVFERTLKLYGGDADSDTNRNRQGQLRQVDPQELLRSGRGIV

Entity 3 polymer

description	Allophycocyanin alpha subunit
formula_weight	17555.1 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,C,E,G,I,K

MSVLTKAIVNADAEARYLSPGELDRIKSFVASGERRLRIAQTLTEARERIVKQAGDQLFQKRPDVVSPGGNAYGEKMTALCLRDLDYYLRLVTYGIVAGDVTPIEEIGIIGVKEMYNSLQTPIPAVAEGVRAMKNVATSLLSGDDAAEAGFYFDYLVGAMQ

Entity 4 polymer

description	Allophycocyanin beta subunit
formula_weight	17241.7 kDa
src_method	nat
entity_count	6

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,J,L

MQDAITAVINNYDVQGKYLDGAALDKLKAYFTTGAVRVRAAAVISSNATTIIKEAAAKALIYSDLTRPGGNMYTTRRYAACIRDMDYFLRYATYAMLAGDPSILDERVLNGLKETYNSLGVPIAATVGGIQAMKEVVGGLVGPDAAKEASIYFDYLSSGLS

Entity 5 polymer

description	Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
formula_weight	7765.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MSRYFKVTACIPSLKRVRTGRELQNTFFTKLVPYENWFTEQQRIQKAGGKVLSVKLFTGVQGANTGVGA

Entity 6 polymer

description	Glr2806 protein
formula_weight	81544.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	X

MSATTYDWRKVIDSIKIEDPVKPGDFANFLDMARGIESRTGVWSISYESLRTLGPPEGGMLRPAVGGTAEAAAQKQLGITAVAPASVVELRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDVEIDSYIDSDEYIETFGENIVPYFRGFKYQTNQSAGGFPRMVKLWGGDAGSDTDRGKNGQRTLVTTKDLIGPTKIFVPFVAPGRDADMVSGDYTRLAFGLSGEAAAQRQLGIASVAPAPICQLRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDVEIDSYIDSDEYIETFGENIVPYFRGFKYQTNQSAGGFPRMVKLWGGDAGSDTDRATGGQRTLVTTRELVKTLPLLTEIPAVPATRGFEQVLNQLKRPAPGGTGEAQGQKQLGITAVAPAPICQLRPNASEEDLQGVLRAVYRQVLGNTYVMESERPTQAESLLRNGSISVREFVRRIAKSDLYKERFFNKASNNRFIELNFKHLLGRAPYNHGEIQEHFGLYHKAGYDAEIDSYIDSDEYLLTFGEDVVPYFRGFKYQTNQSAGGFPRFTKLYGGDAGSDTDRGKNGQRTLVTTKDLVVSGQFSKPV

Entity 7 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	12

▶

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	2.94 Å
resolution_method	—
num_particles	746972

fit	/app/data/saxs_computation/v7/9v7k/9v7k.fit
pddf	/app/data/pr_computation/v7/9v7k/9v7k.pr.out
profile	/app/data/saxs_computation/v7/9v7k/9v7k.dat

Phycobilisome allophycocyanin hexamer C from Gloeobacter violaceus PCC 7421

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

EM 3D

5. Entities & Polymer Info (7)

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 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)