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9t5t

Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203

Method: ELECTRON MICROSCOPY D_max: 196.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t5t
deposition_date	2025-11-05
title	Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203
keywords	Chlorophyll f, photosystem II, ELECTRON TRANSPORT, FaRLiP; 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	57.38 Å
rg_electron	56.72 Å
i0	5077370000.00
molecular_weight	727540.0 kDa
excluded_volume	957970 Å³
envelope_volume	1108000 Å³
shell_volume	152180 Å³
envelope_diameter	212.6 Å
shell_rg	65.08 Å
envelope_rg	57.19 Å
shape_rg	56.71 Å
total_rg	56.92 Å
total_atoms	51566
n_residues	5388
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	196.7 Å
rg_real	57.28 Å
rg_real_error	1.49 Å
i0_real	5.0770e+09
i0_real_error	9.9930e+07
rg_reciprocal	57.44 Å
i0_reciprocal	5079000000.0000
total_estimate	0.8619
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	65.6 Å
skewness	0.331
kurtosis	-0.309
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0004
highest_alpha	741200000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.850

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4. Crystallography & Experiment

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5. Entities & Polymer Info (39)

Entity 1 polymer

description	Photosystem II protein D1
formula_weight	40732.5 kDa
ec_number	1.10.3.9
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,a
atom_count	52226

MTTVLQRQLNRVPAWERFCNWVTSTENRLYIGWFGVLMIPLLGVSICVFTIAFIAAPPVDIDGIREPVSGSLLYGNNIITGAVVPMSNAIGLHFYPIWEAASMDEWLYNGGPYQMIGFHYIPALCCYAGREWELSYRLGMRPWIAVAYTAPVAATSSVFLVYPIGQGSFSDGLPMGISGTFNFMFVFQAEHNILMHPFHMLGVAGVLGGSLFCAMHGSLVTSSLIRETSDNESQNYGYKFGQESETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLAAWPVICIWATALGISTMAFNLNGFNFNNSVLDSQGRVLPTWADVLNRANLGFEVMHERNAHNFPLDLACSDAVPVAFKAPAIAEVPPQAIAS

Entity 2 polymer

description	Photosystem II CP47 reaction center protein
formula_weight	57614.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,b

MGLPWYRVHTSVINDPGRLIAVHLMHNALCAGFAGSMLLFELALYDSSDPVLNPMWRQGCFLMPFVARLGVTNSWQGWSITGESVADPGFWTFETVAIAHIIFSGLEFLAACWHWVYWDLATFFDPKTNEPVLDLPRIFGIHLLLAGLLCFGFGAFHLTGIFGPGMWVSDPYGLTGHVQGVAPVWGAEGFNPYNPGGVVAHHIAAGIVGIIGGLFHIVTRPPEVLYKALRMGNIEGALASGLAVFFFAGFVACGSMWYGTATTPIELWGPTRFQWDQNYFKKEIDRRVQSNLAEGKSLSEAWSAIPEKLAFYDYVGNSPAKGGLFRVGRMVDGDGVAKAWLGHAIFKDGEGRELNVRRMPNFFETFPVVLTDKDDVVRADIPFRRAEAKYSFEQKGVTVSFVGGTLDGQAYTEPSTVKKFARQAQLGEVFDFDRETYNSDGVFRTSNRGFFAFFHCCFALVWFFGHIWHGSRAIFRDVFAGIDPGLDEQVEFGVFQKVGDLTTRKKIPVAAMAGTREPAA

Entity 3 polymer

description	Photosystem II CP43 reaction center protein
formula_weight	50827.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,c

METPFDRSITTTTNVDTPREGRDEASTGYAWWAGNARFINLSGRFLGAHVAHAGLVAFWAGAMLMFEVAHYVPEKPMYEQGLILMPHIATLGFGVGQGGQVVDIFPFFAIAAIHLIGSAVLGFGGVYHSIKGPERLAGFYDFDWTDKDKVTSILGYHLIALGLGALLLVARAMYLGGLYDTWAPGGGDVRVVTNPTLDPRIIFGYLFKGFTGGAGNIASVNNLEDIVGGHIWMGSILIAGGIWHVLTKPFKWAERVFIWSGEAYLSQSLGNVAGQALIAACFIWFNNTAYPSEFYGPTAPEASQAQALNFLVRDQQLGANVVSAQGPTGLGKYLMRSPTGEIIFGGETMRFWDFKGPWLEPLRGPNGLDLEKIRYDIQPWQIRRASEYMTHAPLGSLNSVGGVATEINSFNYVSPRAWLASAHFVFAFLFLVGHLWHAGRARAAAAGFERGIDREDEPVLSMPPLD

Entity 4 polymer

description	Photosystem II D2 protein
formula_weight	39825.6 kDa
ec_number	1.10.3.9
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,d

MTIAIRSTPIGWGWFGVLDDWLKRDRFVFIGWSGLLLFPCSYMAIGGWFTGTTFVTSWYTHGVVSSYLEGCNFLTTAVSTPADSMGHSLLFLWGPEANWDFTRWCQIGGLWSFVTLHGVFGLIGFCLRQMEIARVVGIRPYNALAFTAPISVFVSVFLIYPLGQSSWFFAPSYGVAGIFRFLLFFQAFHNYTLNPFHMMGVAGVLGGALLCAIHGATVENTLFRDTKGFNTFRGFSTTQAEETYSFVTANRYWSQIFGIAFSNKRWLHFFMLFVPVTGLWMSSIGMVGLAFNVRAYDFVSQELRAAEDPEFETFYTKNILLNEGARAWLAPQDQPHEKFQFPEEVLPRGNAL

Entity 5 polymer

description	Cytochrome b559 subunit alpha
formula_weight	9465.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,e

MSGTTGERPFSDIITSVRYWVIHSITIPALFIAGWLFVSTGLAYDVFGTPRPNEYYPQERQELPIVSDRFESRKQIEEFIGK

Entity 6 polymer

description	Cytochrome b559 subunit beta
formula_weight	5065.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	F,f

MNTNQVNQPIQYPIFTVRWLAVHTLAVPTVFFLGAIASMQFIQR

Entity 7 polymer

description	PsbH2'
formula_weight	5323.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,g

MHHIYYFAYGEGQFASTATGVLFGLLAAFLLCVLLIVYASSTYPADRR

Entity 8 polymer

description	Photosystem II phosphoprotein PsbH
formula_weight	7834.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	H,h

MQQPKYQPKKTAPVQYFFRNFNSEAGKVAPGWGTTPLMVGLMLLFFLFLLIILELANASLMVRGIHVGW

Entity 9 polymer

description	Photosystem II reaction center protein I
formula_weight	4377.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,i

MLTLKIVVYIVVGFFLTLFVFGFLSNDPARNPGRRDLD

Entity 10 polymer

description	Photosystem II reaction center protein J
formula_weight	4015.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	J,j

MSGSGRIPLWVVATIAGLGVIVVVGTFFYGSYTHLGSSL

Entity 11 polymer

description	Photosystem II reaction center protein K
formula_weight	6690.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	K,k

MHVNSESCVEKENLSMEAALLLAKLPEAYSILDPLVDVLPLIPLFFLLLAFVWQAAVGFR

Entity 12 polymer

description	Photosystem II reaction center protein L
formula_weight	4762.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	L,l

MPLERSKNPNNQPVELNRTSLYLGLLLIFVLGILFSSYFFN

Entity 13 polymer

description	Photosystem II reaction center protein M
formula_weight	4156.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	M,m

MQVNDLGFVASILFVLVPSVFLIILYIQTASREGKKD

Entity 14 polymer

description	Photosystem II extrinsic protein O
formula_weight	29794.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	O,o

MKYRALIVAFLALCLGFLTACSEPSQVASRELLTYEQIRGTGLANKCPQLSETSRGSIAIDPNQSYRMVELCLEPTSFFIKEEPVNKRQEAEYIAGKLLTRYTSTIDQVQGDLKVNPDKSLTFVEKDGLDFQAITVQLPGGERVPFLFTIKNLVAQTQPGLTSINTSTDFEGKFNVPSYRTANFLDPKGRGVTTGYDNAVALPASADKQGYANVKSAGIENGSISLQVAKVDNATGEVAGTFESIQPSDTDMGAKEALDVKVRGLFYARIEPQA

Entity 15 polymer

description	Photosystem II reaction center protein Y
formula_weight	4505.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	R,r

MDIDLRVAFVLLPVIAAASWALFNIAPAAIRQIQGFFNKEA

Entity 16 polymer

description	Photosystem II reaction center protein T
formula_weight	3654.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	T,t

MESVAYILILALAIGTLFFAIAFREPPRIEKK

Entity 17 polymer

description	Photosystem II extrinsic protein U
formula_weight	16995.4 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	U,u

MQRGRETVKKLIRLLTILSVLVGCLGWLGISQPAIATNLSDFSLRTVPILAVESPARSSNRADAKLATDFGKKIDLNNTNVAAFRRYPGLYPTLARKIVQNAPYENVEDVMELPGLSERQKQTLEANIGNFTVTDVEAAYTMGDDRYNNGIYR

Entity 18 polymer

description	Photosystem II extrinsic protein V
formula_weight	17602.1 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	V,v

MFKRLIGLVMATVMLAFGLVVGSAAAVEMSEAIRTVPLNDSGDTTVLSLKQVQEGKRLFNYACAQCHVGGVTKTNQNVGLDPESLAGASPSRNNIEGLVDYMKNPTTYDGEEEIAEIHPSIKSADIYPAMRNLRDEDLTAIAGHVLLQPKILGDKWGGGKIYY

Entity 19 polymer

description	Photosystem II reaction center protein X
formula_weight	4326.2 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	X,x

MTPSLMNFFFSLLAGLAIVVIPVTVGLIFISQQDKIQRS

Entity 20 polymer

description	Photosystem II reaction center protein Psb30
formula_weight	4660.5 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Y,y

MSGIFDAIGSFQWETLFQLVSVALIMLAGPAVIFVLAFRNGDL

Entity 21 polymer

description	Photosystem II reaction center protein Z
formula_weight	6890.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	Z,z

MLSALFQLALVALVFLSFALVIGVPVAYATPQNWVESKRLLWIGSIAWFGLVIVIGVLNFLVV

Entity 22 non-polymer

description	CA-MN4-O5 CLUSTER
formula_weight	339.8 kDa
src_method	syn
entity_count	2

Entity 23 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 24 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 25 non-polymer

description	CHLOROPHYLL A
formula_weight	893.5 kDa
src_method	syn
entity_count	60

Entity 26 non-polymer

description	CHLOROPHYLL D
formula_weight	895.5 kDa
src_method	syn
entity_count	2

Entity 27 non-polymer

description	PHEOPHYTIN A
formula_weight	871.2 kDa
src_method	syn
entity_count	4

Entity 28 non-polymer

description	BETA-CAROTENE
formula_weight	536.9 kDa
src_method	syn
entity_count	20

Entity 29 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	12

Entity 30 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	4

Entity 31 non-polymer

description	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
formula_weight	787.2 kDa
src_method	syn
entity_count	14

Entity 32 non-polymer

description	DODECYL-BETA-D-MALTOSIDE
formula_weight	510.6 kDa
src_method	syn
entity_count	20

Entity 33 non-polymer

description	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
formula_weight	723.0 kDa
src_method	syn
entity_count	20

Entity 34 non-polymer

description	Chlorophyll F
formula_weight	905.5 kDa
src_method	syn
entity_count	8

Entity 35 non-polymer

description	DIGALACTOSYL DIACYL GLYCEROL (DGDG)
formula_weight	949.3 kDa
src_method	syn
entity_count	6

Entity 36 non-polymer

description	BICARBONATE ION
formula_weight	61.0 kDa
src_method	syn
entity_count	2

Entity 37 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 38 non-polymer

description	HEME C
formula_weight	618.5 kDa
src_method	syn
entity_count	2

Entity 39 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	660

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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	triclinic

resolution	2.17 Å
resolution_method	—
num_particles	49763

fit	/app/data/saxs_computation/t5/9t5t/9t5t.fit
pddf	/app/data/pr_computation/t5/9t5t/9t5t.pr.out
profile	/app/data/saxs_computation/t5/9t5t/9t5t.dat

Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203

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 (39)

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 polymer

Polymer

Entity 19 polymer

Polymer

Entity 20 polymer

Polymer

Entity 21 polymer

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 non-polymer

Entity 35 non-polymer

Entity 36 non-polymer

Entity 37 non-polymer

Entity 38 non-polymer

Entity 39 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)