SAXSdb — 9w4j

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1. Structure Basics

entry_id	9w4j
deposition_date	2025-07-31
title	Cryo-EM structure of CpcL-PBS3
keywords	Phycobilisomes, 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	60.61 Å
rg_electron	60.39 Å
i0	8308940000.00
molecular_weight	764550.0 kDa
excluded_volume	954340 Å³
envelope_volume	1228100 Å³
shell_volume	162640 Å³
envelope_diameter	190.9 Å
shell_rg	66.64 Å
envelope_rg	59.51 Å
shape_rg	60.39 Å
total_rg	60.51 Å
total_atoms	53917
n_residues	6833
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	177.5 Å
rg_real	60.59 Å
rg_real_error	1.00 Å
i0_real	8.3090e+09
i0_real_error	1.4300e+08
rg_reciprocal	60.59 Å
i0_reciprocal	8309000000.0000
total_estimate	0.8360
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	68.3 Å
skewness	0.374
kurtosis	-0.425
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	2999000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.956; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.002

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Photosystem I-associated linker protein CpcL
formula_weight	22399.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	53917

MALPLLEYKPTTQNQRVQSFGTADVNEDTPYIYRLENANSPSEIEELIWAAYRQVFNEQEILKFNRQIGLETQLKNRSITVKDFIRGLAKSERFYQLVVTPNNNYRLVEMSLKRLLGRSPYNEEEKIAWSIQIASKGWGGFVDALIDSTEYEQAFGDNTVPYQRKRLTTDRPFSFTPRYGADYRDRAGIVRP

Entity 2 polymer

description	C-phycocyanin alpha subunit
formula_weight	17475.5 kDa
src_method	nat
entity_count	18

Polymer

type	polypeptide(L)
strand_id	B,D,F,H,J,L,O,Q,S,U,W,Y,N,b,d,f,h,j

MVKTPITEAIAAADTQGRFLGNTELQSARGRYERAAASLEAARGLTSNAQRLIDGATQAVYQKFPYTTQTPGPQFAADSRGKSKCARDVGHYLRIITYSLVAGGTGPLDEYLIAGLAEINSTFDLSPSWYVEALKHIKANHGLSGQAANEANTYIDYAINALS

Entity 3 polymer

description	C-phycocyanin beta subunit
formula_weight	18403.8 kDa
src_method	nat
entity_count	18

Polymer

type	polypeptide(L)
strand_id	C,E,G,I,K,M,P,R,T,V,X,Z,a,c,e,g,i,k

MTLDVFTKVVSQADSRGEFLSNEQLDALANVVKEGNKRLDVVNRITSNASAIVTNAARALFEEQPQLIAPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDASVLDDRCLNGLRETYQALGTPGSSVAVGVQKMKDAAVGIANDPNGITKGDCSQLISEVASYFDRAAAAVG

Entity 4 polymer

description	Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
formula_weight	32254.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	2,3

MAITTAASRLGTEPFSDAPKVELRPKASREEVESVIRAVYRHVLGNDYILASERLVSAESLLRDGNLTVREFVRSVAKSELYKKKFFYNSFQTRLIELNYKHLLGRAPYDESEVVYHLDLYQNKGYDAEIDSYIDSWEYQSNFGDNVVPYYRGFETQVGQKTAGFNRIFRLYRGYANSDRAQVEGTKSRLARELASNKASTIVGPSGTNDSWGFRASADVAPKKNLGNAVGEGDRVYRLEVTGIRSPGYPSVRRSSTVFIVPYERLSDKIQQVHKQGGKIVSVTSA

Entity 5 polymer

description	Phycobilisome 34.5 kDa linker polypeptide, phycoerythrocyanin-associated, rod
formula_weight	7233.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	4

AAPTLISSATKGDNRMFVIEAIAGGLNTNVAVRRSRQVYTVSYERLSATYQEIHKRGGKIVKISQV

Entity 6 non-polymer

description	PHYCOCYANOBILIN
formula_weight	588.7 kDa
src_method	syn
entity_count	54

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6. Citations (1)

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resolution	2.93 Å
resolution_method	—
num_particles	74453

fit	/app/data/saxs_computation/w4/9w4j/9w4j.fit
pddf	/app/data/pr_computation/w4/9w4j/9w4j.pr.out
profile	/app/data/saxs_computation/w4/9w4j/9w4j.dat

Cryo-EM structure of CpcL-PBS3

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

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)