SAXSdb — 9v7h

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1. Structure Basics

entry_id	9v7h
deposition_date	2025-05-28
title	Phycobilisome rod R2 from Gloeobacter violaceus PCC 7421
keywords	Phycobilisome, PHOTOSYNTHESIS; PHOTOSYNTHESIS
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	49.81 Å
rg_electron	49.18 Å
i0	3824540000.00
molecular_weight	518240.0 kDa
excluded_volume	648200 Å³
envelope_volume	837860 Å³
shell_volume	131390 Å³
envelope_diameter	152.6 Å
shell_rg	60.29 Å
envelope_rg	48.20 Å
shape_rg	49.18 Å
total_rg	49.47 Å
total_atoms	36476
n_residues	4575
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	145.6 Å
rg_real	49.54 Å
rg_real_error	0.68 Å
i0_real	3.8250e+09
i0_real_error	6.8250e+07
rg_reciprocal	50.02 Å
i0_reciprocal	3827000000.0000
total_estimate	0.8626
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.2 Å
skewness	0.040
kurtosis	-0.578
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	2025000000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.387

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phycocyanin-associated rod linker protein
formula_weight	31085.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	36476

MSVLTGDNQQRGSKLFKITIALSPTLAHHPWPGLDTHEPSQSSYSTIVSLERLLPEMTRIKRNGGRILEITEGEASESRANFPAVMEPPVVELYPRAGEAEVQAVIAVAYKQVFGNIHVMESERIVSAESLLRNRSISVREFVRLLAKSDLYKESFFHCTSNNRFIELNFKHLLGRAPYNHSEIIEHLDRYQSQGYDAEIDSYIDSDEYVKTFGENVVPYHRGFKSQVGQQSVAAFERMIRLFGGDASSDTSLNRTGQKRLVDPKQLLRSGRGIV

Entity 2 polymer

description	Phycocyanin beta chain
formula_weight	18479.0 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,J,L,O,Q,S,U,W,Y

MQDAFTKAIVAADLRGSFLSEQELNQLTNLVKESNKRLDAVNAITGNAAEIISDAAHKLFAEQTDLIRPGGNAYPNRRMAACLRDMEIILRYVSYALLAGDASVLEDRCLNGLKETYVALGTPTRSVARAVQLMKETAIGYVNSPSGVTRGDCSALVNEAATYFDKAAASIA

Entity 3 polymer

description	Phycocyanin alpha chain
formula_weight	17679.9 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	C,E,G,I,K,N,P,R,T,V,X,a

MKTVITEVIASADSQGRFLNNTELQAANGRFQRATASMEAARALTSNADSLVKGAVQEVYNKFPYLTQPGQMGYGDTNQAKCARDISHYLRFITYSLVAGGTGPLDDYIVAGLREVNRTFNLSPSWYIEALKHIKGKVGSQLSGQPLTEANAYIDYCINALS

Entity 4 polymer

description	Phycocyanin-associated rod linker protein
formula_weight	30913.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MNVLTTSSQRGGKLFKVTMTLSPALSHHPWPSLDTYEPSQNSYSVVVPLDRLLAEMTYIKNKGGRVLDISPADLEALGPPDISSVAIPLKVELWAKADVSDVQAAIVAAYKQIFGNTYVLESERLTSAESLLRNGSISVREFVRLLAKSELYKERFFFCTSNNRFTELNFKHFLGRAPYNQSEIAAHLDRYQTFGYDAEIDSYIDSDEYIQAFGENVVPYYRGFKSQSGQTVESFNRMFKLYRGDAGSDTNLNLQGQKRRVDPKNLLRSGRGIV

Entity 5 polymer

description	Glr1262 protein
formula_weight	92127.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MSTVLDDQSKAYAPGSANGPTAGLEPFVRMSRMIRSGVPEDREEPDELWLSMVRDIFGRGYMDRLSQTRAIDYSAFVRPADQATADGAAQTKLGITAIAPDQGVELRPNFTEADVITVIRAAYKQLFGNTYILESERVIQAESLLRNGSISVREFIRILAKSDLYKERFFRCTSNNRFIELNLKHLLGRAPYNQGEIAEHLDRYCQSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQSAAAFERMRALYSGDAGSDTDRNQNGQRTELTSGLADPAQPVRARTDYALTRVDIPGGNGAAGRLAALDESLGSWLDAARDLISQNDYSQKAIEVEPKRVAPYAQYLTPAVEATPDAAAQTKLGITAVAPDQAVELRPNFGEAEVQAVIRAAYKQIFGNTYILEADRVVIAESLLRNGSISVREFVRLLAKSDLYRDRFFRTASNNRFIELNFKHFLGRAPYSQAEIGEHFNRYHKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQVGQAARGFDQMQQLFAGDAGSDTDRGIGAQPAAKLTFPLSRPLGVTSAYFPSSQGGAATSDGLEMFTRMARELTVTPVSARRTTSPTAPTAPAMPLAGYYSRPAPRATADGDAQTKLGITAVAPAQAVELRPNFGETELQAVIRATYKQLFGNTYILEADRVVQAESLLRNGSINVREFVRLLAKSELYKERFFHCTSNNRFIELTFKHLLGRAPYNQSEFVEHLDRYQKSGYDAEIDSYIDSDEYRRVFGENTVPYFRGFKYQTGQAAGVFERTLKLYGGDADSDTNRNRQGQLRQVDPQELLRSGRGIV

Entity 6 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	36

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6. Citations (1)

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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	2.950 Å
resolution_low	2.950 Å
r_factor	—
r_work	0.3064
r_free	—

resolution	2.95 Å
resolution_method	—
num_particles	207644

fit	/app/data/saxs_computation/v7/9v7h/9v7h.fit
pddf	/app/data/pr_computation/v7/9v7h/9v7h.pr.out
profile	/app/data/saxs_computation/v7/9v7h/9v7h.dat

Phycobilisome rod R2 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

Refinement

EM 3D

5. Entities & Polymer Info (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)