SAXSdb — 9x6d

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1. Structure Basics

entry_id	9x6d
deposition_date	2025-10-15
last_revision	2026-04-01
title	The cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942
keywords	phycobilisome PBS, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	48.14 Å
rg_electron	47.27 Å
i0	3617250000.00
molecular_weight	505290.0 kDa
excluded_volume	632420 Å³
envelope_volume	766450 Å³
shell_volume	124530 Å³
envelope_diameter	144.0 Å
shell_rg	58.59 Å
envelope_rg	46.53 Å
shape_rg	47.27 Å
total_rg	47.57 Å
total_atoms	35641
n_residues	4557
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	142.7 Å
rg_real	47.70 Å
rg_real_error	0.57 Å
i0_real	3.6170e+09
i0_real_error	5.7190e+07
rg_reciprocal	48.14 Å
i0_reciprocal	3619000000.0000
total_estimate	0.8770
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	64.8 Å
skewness	0.051
kurtosis	-0.563
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0001
highest_alpha	1573000000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.621

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phycobilisome rod-core linker polypeptide
formula_weight	28372.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	35641

MALPLLNYAPTTQNSRVAGFEVPGDEQPKQYNTEDQYSPVQFDEVIQAAYRQIFFHAFKCDRQTVLESQLRNGQITVRDFIRGLLLSATFRSSFYDKNSNYRFVEQVVQRVLGRDVYGEREKIAWSLAVATQGYEGFIDTLLNSDEYLSNFGYDKVPYQRRRVLPGRALGETPFNIKSPRYDSYYRTILGFPKAVFAGGPGKRFPAQYLSAKAGDPGAYLALARSIGARGQALSASADIDYLSKVPYRKR

Entity 2 polymer

description	C-phycocyanin alpha subunit
formula_weight	17303.2 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	B,F,G,H,I,K,N,R,S,T,U,W

MSKTPLTEAVAAADSQGRFLSSTELQVAFGRFRQAASGLAAAKALANNADSLVNGAANAVYSKFPYTTSTPGNNFASTPEGKAKCARDIGYYLRIVTYALVAGGTGPIDEYLLAGLDEINKTFDLAPSWYVEALKYIKANHGLSGDSRDEANSYIDYLINALS

Entity 3 polymer

description	C-phycocyanin beta subunit
formula_weight	18287.7 kDa
src_method	nat
entity_count	12

Polymer

type	polypeptide(L)
strand_id	C,D,E,J,L,M,O,P,Q,V,X,a

MTFDAFTKVVAQADARGEFLSDAQLDALSRLVAEGNKRIDTVNRITGNASSIVANAARALFAEQPSLIAPGGNAYTNRRMAACLRDMEIILRYVTYAVFTGDASILDDRCLNGLRETYLALGVPGASVAEGVRKMKDAAVAIVSDRNGITQGDCSAIISELGSYFDKAAAAVA

Entity 4 polymer

description	Phycobilisome rod linker polypeptide
formula_weight	30392.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Y

MTSLEAARRLGFSAYSESAPLEWRAGASSDEINAIIRAVYRQVLGNDYVMSTERLTSAESLLRGGEISVRDFVRAVALSELYREKFFHNNAHNRFIELNFKHLLGRAPYDQAEVAAHAATYHSHGYDADINSYIDSAEYTESFGDNVVPYFRGFATIRAQKTVGFNRIFQLYRGYATSDRSATSQRSRLDQEVARNAASPVLIGSTGSALVGTCGGSRDQLFRVQVQQQGVTARTSNRIRRSNATYFVSYEKLNATLQRVHAQGGRIVSITPA

Entity 5 polymer

description	Phycobilisome rod linker polypeptide
formula_weight	31734.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MAITVASSRLGTAPFSNAAPVELRPDGDRDQVQAVIRAVYRQVLGNDYIMKSERLTAAESLLVNGSISVRDFVRAVAKSELYKTKFFYNNFQTRVIELHCKHLLGRAPYSEAEVIEHLDRYETQGYDADVDSYIDSSEYLETFGESIVPYYRDIEYHVGQQSVGLPRLFSLYRGYATSDRTSLGGNNSRLAANLAAKSVAPVVAPSVGTNYVASTKGEAPMRALGGSTPFGQTASRIFRVEIAAISKPGFPSVRRSNRSLLVPYEQLNNTLQQVNRSGGRVVSVAPASL

Entity 6 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	34

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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	2.920 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.92 Å
resolution_method	—
num_particles	258722

fit	/app/data/saxs_computation/x6/9x6d/9x6d.fit
pddf	/app/data/pr_computation/x6/9x6d/9x6d.pr.out
profile	/app/data/saxs_computation/x6/9x6d/9x6d.dat

The cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942

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)