SAXSdb — 9v7i

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1. Structure Basics

entry_id	9v7i
deposition_date	2025-05-28
title	Phycobilisome rod R3 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	49.99 Å
rg_electron	49.13 Å
i0	3826350000.00
molecular_weight	517740.0 kDa
excluded_volume	647350 Å³
envelope_volume	836580 Å³
shell_volume	131320 Å³
envelope_diameter	148.2 Å
shell_rg	60.24 Å
envelope_rg	48.13 Å
shape_rg	49.13 Å
total_rg	49.42 Å
total_atoms	36438
n_residues	4567
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	143.7 Å
rg_real	49.50 Å
rg_real_error	0.67 Å
i0_real	3.8260e+09
i0_real_error	7.0860e+07
rg_reciprocal	49.98 Å
i0_reciprocal	3829000000.0000
total_estimate	0.8538
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	67.4 Å
skewness	0.039
kurtosis	-0.583
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	1975000000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.246

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phycobilisome rod linker polypeptide CpcC1
formula_weight	31085.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	36438

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	Phycobilisome rod linker polypeptide CpcC2
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	3.030 Å
resolution_low	3.030 Å
r_factor	—
r_work	0.3276
r_free	—

resolution	3.03 Å
resolution_method	—
num_particles	746972

fit	/app/data/saxs_computation/v7/9v7i/9v7i.fit
pddf	/app/data/pr_computation/v7/9v7i/9v7i.pr.out
profile	/app/data/saxs_computation/v7/9v7i/9v7i.dat

Phycobilisome rod R3 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)