SAXSdb — 9w7k

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1. Structure Basics

entry_id	9w7k
deposition_date	2025-08-06
title	Cryo-EM structure of CpcL-PBS2
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	48.82 Å
rg_electron	47.94 Å
i0	3731800000.00
molecular_weight	508520.0 kDa
excluded_volume	634820 Å³
envelope_volume	788960 Å³
shell_volume	126560 Å³
envelope_diameter	146.9 Å
shell_rg	59.16 Å
envelope_rg	47.15 Å
shape_rg	47.93 Å
total_rg	48.25 Å
total_atoms	35862
n_residues	4543
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	140.8 Å
rg_real	48.36 Å
rg_real_error	0.70 Å
i0_real	3.7320e+09
i0_real_error	5.4540e+07
rg_reciprocal	48.81 Å
i0_reciprocal	3734000000.0000
total_estimate	0.8539
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	66.0 Å
skewness	0.051
kurtosis	-0.567
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	1245000000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.950; Smooth: 0.259

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Photosystem I-associated linker protein CpcL
formula_weight	22267.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	1
atom_count	35862

ALPLLEYKPTTQNQRVQSFGTADVNEDTPYIYRLENANSPSEIEELIWAAYRQVFNEQEILKFNRQIGLETQLKNRSITVKDFIRGLAKSERFYQLVVTPNNNYRLVEMSLKRLLGRSPYNEEEKIAWSIQIASKGWGGFVDALIDSTEYEQAFGDNTVPYQRKRLTTDRPFSFTPRYGADYRDRAGIVRP

Entity 2 polymer

description	Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
formula_weight	32122.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	2,3

AITTAASRLGTEPFSDAPKVELRPKASREEVESVIRAVYRHVLGNDYILASERLVSAESLLRDGNLTVREFVRSVAKSELYKKKFFYNSFQTRLIELNYKHLLGRAPYDESEVVYHLDLYQNKGYDAEIDSYIDSWEYQSNFGDNVVPYYRGFETQVGQKTAGFNRIFRLYRGYANSDRAQVEGTKSRLARELASNKASTIVGPSGTNDSWGFRASADVAPKKNLGNAVGEGDRVYRLEVTGIRSPGYPSVRRSSTVFIVPYERLSDKIQQVHKQGGKIVSVTSA

Entity 3 polymer

description	C-phycocyanin alpha subunit
formula_weight	17344.3 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

VKTPITEAIAAADTQGRFLGNTELQSARGRYERAAASLEAARGLTSNAQRLIDGATQAVYQKFPYTTQTPGPQFAADSRGKSKCARDVGHYLRIITYSLVAGGTGPLDEYLIAGLAEINSTFDLSPSWYVEALKHIKANHGLSGQAANEANTYIDYAINALS

Entity 4 polymer

description	C-phycocyanin beta subunit
formula_weight	18272.6 kDa
src_method	nat
entity_count	12

Polymer

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

TLDVFTKVVSQADSRGEFLSNEQLDALANVVKEGNKRLDVVNRITSNASAIVTNAARALFEEQPQLIAPGGNAYTNRRMAACLRDMEIILRYVTYAILAGDASVLDDRCLNGLRETYQALGTPGSSVAVGVQKMKDAAVGIANDPNGITKGDCSQLISEVASYFDRAAAAVG

Entity 5 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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resolution	2.58 Å
resolution_method	—
num_particles	270378

fit	/app/data/saxs_computation/w7/9w7k/9w7k.fit
pddf	/app/data/pr_computation/w7/9w7k/9w7k.pr.out
profile	/app/data/saxs_computation/w7/9w7k/9w7k.dat

Cryo-EM structure of CpcL-PBS2

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 (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)