← Back to search

9t5u

Chlorophyll f-containing monomeric far-red Photosystem II from Calothrix sp. NIES-3974

Method: ELECTRON MICROSCOPY D_max: 128.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9t5u
deposition_date	2025-11-06
title	Chlorophyll f-containing monomeric far-red Photosystem II from Calothrix sp. NIES-3974
keywords	Chlorophyll f, photosystem II, ELECTRON TRANSPORT, FaRLiP; ELECTRON TRANSPORT
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	40.91 Å
rg_electron	39.74 Å
i0	848089000.00
molecular_weight	300180.0 kDa
excluded_volume	398730 Å³
envelope_volume	449080 Å³
shell_volume	87336 Å³
envelope_diameter	138.6 Å
shell_rg	49.58 Å
envelope_rg	39.97 Å
shape_rg	39.74 Å
total_rg	40.28 Å
total_atoms	21332
n_residues	2174
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

▼

3. P(r) Analysis (GNOM)

dmax	128.8 Å
rg_real	40.71 Å
rg_real_error	1.07 Å
i0_real	8.4810e+08
i0_real_error	1.4160e+07
rg_reciprocal	40.91 Å
i0_reciprocal	848300000.0000
total_estimate	0.8878
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	52.9 Å
skewness	0.154
kurtosis	-0.395
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	87970000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.919

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (34)

Entity 1 polymer

description	PsbA
formula_weight	40209.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	21449

MTTISQPKTTRFPAWERFCDWITSTENRLYIGWFGVLMIPLLGVSICVFVIAFIAAPPVDIDGIREPVAGSIFYGNNIITAAVVPMSNAIGLHFYPIWEAASMDEWLYNGGPYQMIAFHYIPALACYMGREWELSYRLGMRPWIAVAYSAPLAATTSVFLIYPIGQGSFSDGLPMGISGTFNFMFVFQAEHNILMHPLHMIGVAGVLGGSLFCAMHGSLVTSSIIRETTELESQNYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVICIWGTAIGISTMAFNLNGFNFNNSILDSQGRVLPSWADVLNRANLGFEVMHERNAHNFPLDLASGEAIPVPVAMAAPSITM

Entity 2 polymer

description	PsbB
formula_weight	56801.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MGLPWYRVHTVVLNDPGRLIAVHLMHTALTAGWAGSMALYELALFDPSDSVFNPMWRQGMFVLPFMTRLGITQSWAGWNITGEAVNGFTLWTFESVAAAHIILAGLLFLAACWHWVYWDLELFQDPKSGESFLDLPKIFGIHLLLAGLLCFGFGAFHLTGIFGPGMWVSDPYGLTGHIQGVAPEWGPDGFNPYNPGGVVAHHIAAGIVGIIGGIFHISVRPPEVLYRTLRMGNIETVLASALATFFFAAFVVSGTMWYGTATTPIELFGPTRYQWDSSYFQTEISRRVQTSLNQGATLAEAWSNIPDKLAFYDYVGNSPAKGGLFRVGPMVKGDGVALSWLGHPVFQDREGRELIVRRMPNFFETFPVVLTDKDNIVRADIPFRRADSKLSFEQTGVTVSFLGGALNGQTFSDPVEVKKYARRAQLGEIFAFDTQTFKSDGIFRTSTRGWFAFAHACWGLLWFFGHIWHGARTIFRDVFAGIDPELDEEQVEFGVFQKVGDVSTRKKQLV

Entity 3 polymer

description	PsbC
formula_weight	50618.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

METPLDISITTTISPPASEGRDEPSTGYAWWAGNARFVNKSGRFLGAHVAHAGLVAFWAGAMLLFEVAHYTPEKPMYEQGLILMPHIATLGIGVGHGGEVTDIFPFFAIAVAHLIGSAVLGFGGLYHSLKGPEKLAGFFDFDWRDKNKVTSILGFHLIALGVAAYLLVGKAMIWGGLYDTWAPGGGDVRLVTNPTLDPRIIFGYLLKPFTGGQGSIVSVNNLEDLVGGHIWIGGILILGGIWHIITEPFKWTHKVFIWSGEAYLSQSLGNVAGQAIIATMFIWFNNTAYPSEFYGPTAPEASQAQALIFVVRDQKLGANVASAQGPTGLGKYLMRSPTGEIIFGGETMRFWDVRAPWLEPLRGPNGLDIKKIQNDIQPWQIRRAAEYMTHAPLGSLNSVGGVATEINSFNFVSPRTWLAAAHFVFFLLFLVGHLWHAGRARAAAAGFERGLDRQDEPVLSMKPLD

Entity 4 polymer

description	PsbD
formula_weight	39942.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MTIAIRPTQSNWRWFYILDDWLKRDRFVFIGWSGLLLFPCAYLAIGGWFTGTTFVSSWYTHGVVSSYLEGCNFLTAAVSTPADSMGHSLLLLWGPEAEGNITRWFQIGGLWNFVAFHGVFGLIGFMLRQFEIARTIGIRPYNAIAFSAPIAVFVSVFLIYPLGQSSWFFAPSFGVAAIFRFLLFFQAFHNYTLNPFHMMGVAGVLGGALLCAIHGATVENTLFKDTTGFNTFRGFSTTQAEETYSFVTANRYWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSAIGMVGLAFNLRAYDFISQELRAAEDPEFETFYTKNILLNEGARAWMAPQDQPHEHFQFPEEVLPRGNAL

Entity 5 polymer

description	PsbE
formula_weight	9382.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MSGTTGERPFGDIITSIRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPNEYFTQTRQELPIVSDRYESKKQVEQFIGK

Entity 6 polymer

description	PsbF
formula_weight	5224.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MTSSNNLNQPVQQYPIFTVRWLAVHTLAVPTVFFLGAIAAMQFIQR

Entity 7 polymer

description	PsbH
formula_weight	7636.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MAQRTRLGDILRPLNSEYGKVAPGWGTTPLMAVFMGLFFVFLLIILQLYNKSIIIQDVMVDWRSLGN

Entity 8 polymer

description	PsbI
formula_weight	4367.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MLALKVVVYIVVAFFVSLFVFGFLSNDPARNPGRRDFE

Entity 9 polymer

description	PsbJ
formula_weight	3872.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MSGGGRIPLWIVATVAGLGVITVVGIFFYGAYAGLGSSI

Entity 10 polymer

description	PsbK
formula_weight	5062.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MEAAILLAKLPEAYQIFDPLVDVLPIIPVFFLLLAFVWQAAVGFR

Entity 11 polymer

description	PsbL
formula_weight	4546.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MERTPNPNNQPVELNRTSLFLGLLLIFVLGILFSSYFFN

Entity 12 polymer

description	PsbM
formula_weight	4300.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	M

MQVNDLGFVASLLFVLVPSVFLIILYTLTASREGGQKDN

Entity 13 polymer

description	PsbY
formula_weight	4444.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	R

MDIDFRIAIVLAPIAVAAGWAVFNIGRAALVQLQNFLNKEA

Entity 14 polymer

description	PsbT
formula_weight	3973.8 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	T

MESIAYVLIFAVTLGILFFAIAFREPPRIQKKEK

Entity 15 polymer

description	PsbX
formula_weight	4381.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	X

MTPSLANFLWSLFWGTVIVVIPATVALIFISQSDKIQRS

Entity 16 polymer

description	Ycf12
formula_weight	4421.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Y

MFEALASIKWEVIFQLTAVALIMLSGPIVIFLLAVRKGDL

Entity 17 polymer

description	PsbZ
formula_weight	6740.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Z

MTFIFQFALLALVVVSFAMVIGVPVAYATPQSWVESKKLLWLGSAVWAALVVLVGILNFLVV

Entity 18 non-polymer

description	CA-MN4-O5 CLUSTER
formula_weight	339.8 kDa
src_method	syn
entity_count	1

Entity 19 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 20 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 21 non-polymer

description	CHLOROPHYLL A
formula_weight	893.5 kDa
src_method	syn
entity_count	32

Entity 22 non-polymer

description	CHLOROPHYLL D
formula_weight	895.5 kDa
src_method	syn
entity_count	1

Entity 23 non-polymer

description	PHEOPHYTIN A
formula_weight	871.2 kDa
src_method	syn
entity_count	2

Entity 24 non-polymer

description	BETA-CAROTENE
formula_weight	536.9 kDa
src_method	syn
entity_count	10

Entity 25 non-polymer

description	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
formula_weight	795.1 kDa
src_method	syn
entity_count	3

Entity 26 non-polymer

description	;2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE ;
formula_weight	749.2 kDa
src_method	syn
entity_count	2

Entity 27 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	4

Entity 28 non-polymer

description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
formula_weight	787.2 kDa
src_method	syn
entity_count	7

Entity 29 non-polymer

description	Chlorophyll F
formula_weight	905.5 kDa
src_method	syn
entity_count	2

Entity 30 non-polymer

description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
formula_weight	723.0 kDa
src_method	syn
entity_count	7

Entity 31 non-polymer

description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
formula_weight	949.3 kDa
src_method	syn
entity_count	5

Entity 32 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	1

Entity 33 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 34 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	117

▶

6. Citations (1)

▶

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	triclinic

resolution	2.33 Å
resolution_method	—
num_particles	285844

fit	/app/data/saxs_computation/t5/9t5u/9t5u.fit
pddf	/app/data/pr_computation/t5/9t5u/9t5u.pr.out
profile	/app/data/saxs_computation/t5/9t5u/9t5u.dat

Chlorophyll f-containing monomeric far-red Photosystem II from Calothrix sp. NIES-3974

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 (34)

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 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Entity 17 polymer

Polymer

Entity 18 non-polymer

Entity 19 non-polymer

Entity 20 non-polymer

Entity 21 non-polymer

Entity 22 non-polymer

Entity 23 non-polymer

Entity 24 non-polymer

Entity 25 non-polymer

Entity 26 non-polymer

Entity 27 non-polymer

Entity 28 non-polymer

Entity 29 non-polymer

Entity 30 non-polymer

Entity 31 non-polymer

Entity 32 non-polymer

Entity 33 non-polymer

Entity 34 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)