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9x69

The structure of phycobilisome with a bicylindrical core from the cyanobacterium Synechococcus elongatus PCC 7942

Method: ELECTRON MICROSCOPY D_max: 267.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9x69
deposition_date	2025-10-15
last_revision	2026-04-01
title	The structure of phycobilisome with a bicylindrical core from the cyanobacterium 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	69.16 Å
rg_electron	68.97 Å
i0	14674800000.00
molecular_weight	1042700.0 kDa
excluded_volume	1310800 Å³
envelope_volume	1696700 Å³
shell_volume	194480 Å³
envelope_diameter	232.3 Å
shell_rg	75.92 Å
envelope_rg	67.91 Å
shape_rg	68.96 Å
total_rg	69.09 Å
total_atoms	73424
n_residues	9306
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	267.4 Å
rg_real	73.15 Å
rg_real_error	2.07 Å
i0_real	1.4810e+10
i0_real_error	3.3400e+08
rg_reciprocal	69.16 Å
i0_reciprocal	14670000000.0000
total_estimate	0.8599
solution_quality	GOOD a GOOD solution
n_peaks	0
r_peak_primary	— Å
skewness	0.615
kurtosis	0.222
angular_range	— – 0.1150 Å⁻¹
current_alpha	0.7744
highest_alpha	3620000000.0000
n_real_points	24
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.637; Stabil: 0.866; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
formula_weight	7821.2 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	0,Y,Z,z
atom_count	73424

MRMFRITACLPSPSKIRTQRELQNTFFTKLVPYDAWFREQQRIQKLGGKIIKVELATGRPNTNTGLL

Entity 2 polymer

description	ApcG
formula_weight	11365.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	1,b

MVLDKLFGKKEKFFLEIDSSAASTETAAVETAVTPVAAAVETPTAAAGVATPEPAATPAPEPVAEETPAKEIPNVTFAADLSVPTINTGRRLPGPSLDPFVQIASEVVRR

Entity 3 polymer

description	Phycobilisome rod-core linker polypeptide
formula_weight	28372.9 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	2,3,4,5

MALPLLNYAPTTQNSRVAGFEVPGDEQPKQYNTEDQYSPVQFDEVIQAAYRQIFFHAFKCDRQTVLESQLRNGQITVRDFIRGLLLSATFRSSFYDKNSNYRFVEQVVQRVLGRDVYGEREKIAWSLAVATQGYEGFIDTLLNSDEYLSNFGYDKVPYQRRRVLPGRALGETPFNIKSPRYDSYYRTILGFPKAVFAGGPGKRFPAQYLSAKAGDPGAYLALARSIGARGQALSASADIDYLSKVPYRKR

Entity 4 polymer

description	Allophycocyanin, beta subunit
formula_weight	17408.7 kDa
src_method	nat
entity_count	22

Polymer

type	polypeptide(L)
strand_id	A,B,C,F,K,L,M,O,T,V,X,a,c,d,g,l,m,n,p,u,w,y

MQDAITAVINASDVQGKYLDSSALDRLKSYFQSGELRVRAAATISANSALIVKEAVAKSLLYSDITRPGGNMYTTRRYAACIRDLEYYLRYATYAMLAGDTSILDERVLNGLKETYNSLGVPIGATVQAIQAIKEVTASLVGPDAGREMGVYLDYISSGLS

Entity 5 polymer

description	Allophycocyanin alpha chain
formula_weight	17439.7 kDa
src_method	nat
entity_count	20

Polymer

type	polypeptide(L)
strand_id	D,E,G,H,I,J,Q,R,U,W,e,f,h,i,j,k,r,s,v,x

MSIVSKSIVNADAEARYLSPGELERIKTFVVGGDRRLRIAQTIAESRERIVKQAGNQLFQKRPDVVSPGGNAYGEDMTATCLRDLDYYLRLVTYGVVSGDITPIEEIGIVGVREMYKSLGTPIEAVAEGVRELKSAATALLTGEDADEAGAYFDYVIGALS

Entity 6 polymer

description	Phycobiliprotein ApcE
formula_weight	78910.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	N,o

MTVTASGGSSLARPQLYQTVPGSTIVQAEQQDRFPQQGELRELSSYFQSGLKRLAIAEIITRNSDTIVSRAANRIFVGGSPLAYIERPKVDPRNLRSAEEQRAREAKLGTVTFVESSGGGGFFSGLTAALGGAGAVRIPSGFRPINVARYGPRNMQKSLRDMSWFLRYITYAIVAGDPNILVVNVRGLREIIEKACSTPATLVALQDMRATSAGYFRNDPEAQQLVKDYFDVLIREFEAPTPSLKQRQRFAEDQQGLALPQSYANAAERRPKFVIKSTLSTVEKNEAIKAAYRQVFERDITRAYSQKVSDLESKVKNGEISTKEFIRRLGKSPLYRQQFHDRFVNSRVIELAFRHFLGRGISSAEEFTRYFDLLSAKGFAALIDALVDSQEYADYFGEETVPYLRGLGQEAQECRNWGVQQELFKYSAPFVKVPQFVTLFGEYKQPLLDQHPYGAGNDPLEIQFGAIFPSRTVNNRTNPAPFGKDTRRLLVSKGGVNNQVGSAAFQQSGTTPTKIFKLTQVAAGSSSIRSKSVGNPSIRQTESTTQAVIRAAYRQVFGRDLYEGQRLTVPEIKLENGEITVREFVRQIAKSETFRKLYWNNLYVVKAVEYIHRRLLGRPTTGRAEINAYFDISAKKGFYALVDAILDSPEYIAAFGEDTVPYERYITPKGLALRSVRGLEASEKVKASLRPAAGAQERRPEVGRR

Entity 7 polymer

description	Allophycocyanin, beta subunit
formula_weight	18590.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	P,q

MRDAVSSLIAGYDLAGKYLDRNAVDSLRAYFAEGNARVQAAEIINANAASLVRDASAQLFEEVPELLRPGGNAYTTRRYSACLRDLDYYLRYATYALVAGNTEVLDERVLQGLRETYTSLGVPSGPTVRGIAILRDRVRQLVEQAGISNAAFVEVPFDHLGRNLAEQDI

Entity 8 polymer

description	Allophycocyanin alpha-B chain
formula_weight	18149.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	S,t

MTIVSQVILKADDELRYPSGGELKNITDFFKTGEQRLRIAQVLSDSEKKIVDQASRKLWQRRPDFIAPGGNAYGQRQRAQCLRDYGWYLRLITYGVLAGDKEPIESIGLLGAREMYNSLGVPLPGMAEAIRTLKEASLALLSSADATVAAPYFDFLIQGMETI

Entity 9 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	48

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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	3.00 Å
resolution_method	—
num_particles	258722

fit	/app/data/saxs_computation/x6/9x69/9x69.fit
pddf	/app/data/pr_computation/x6/9x69/9x69.pr.out
profile	/app/data/saxs_computation/x6/9x69/9x69.dat

The structure of phycobilisome with a bicylindrical core from the cyanobacterium 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

EM 3D

5. Entities & Polymer Info (9)

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 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)